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Egorova A, Zubkov E, Makarov V. Vindeburnol: A natural product-inspired chemical tool for central nervous system drug design. Eur J Med Chem 2024; 280:116966. [PMID: 39413442 DOI: 10.1016/j.ejmech.2024.116966] [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: 04/23/2024] [Revised: 10/10/2024] [Accepted: 10/11/2024] [Indexed: 10/18/2024]
Abstract
Natural products (NPs) often act as sources of CNS-active agents and provide inspiration for the development of synthetic molecules that incorporate their best features. Vindeburnol (VIND; (±)-(3α,14β)-20,21-dinoreburnamenin-14-ol; developmental codes RU24722 or BC19), based on the core structure of eburnamine-vincamine alkaloids, has been extensively investigated for its biological activities. This molecule has demonstrated potential therapeutic properties in various in vivo models of CNS disorders such as multiple sclerosis, Alzheimer's disease, and depressive-like behavior. Although few clinical trials were conducted, further development of vindeburnol was abandoned. This review presents synthetic approaches to vindeburnol synthesis as well as the most complete discussion of its pharmacological effects. Studies involving vindeburnol in animal models of CNS disorders and a few human trials have been presented in separate sections. Special attention is placed on derivatives and analogs based on the vindeburnol scaffold. The interesting pharmacological profile of vindeburnol suggests that this NP-inspired compound may serve as a useful tool or structural basis for next-generation molecules in CNS drug design and discovery.
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Affiliation(s)
- Anna Egorova
- Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences (Research Centre of Biotechnology RAS), 33-2 Leninsky Prospect, 119071, Moscow, Russia
| | - Eugene Zubkov
- Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences (Research Centre of Biotechnology RAS), 33-2 Leninsky Prospect, 119071, Moscow, Russia; V. Serbsky National Medical Research Center for Psychiatry and Narcology, 23 Kropotkinsky Pereulok, 119034, Moscow, Russia
| | - Vadim Makarov
- Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences (Research Centre of Biotechnology RAS), 33-2 Leninsky Prospect, 119071, Moscow, Russia.
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2
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Bharate SB, Lindsley CW. Natural Products Driven Medicinal Chemistry. J Med Chem 2024; 67:20723-20730. [PMID: 39629819 DOI: 10.1021/acs.jmedchem.4c02736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2024]
Affiliation(s)
- Sandip B Bharate
- Department of Natural Products & Medicinal Chemistry, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad-500007, India
| | - Craig W Lindsley
- Vanderbilt Institute of Chemical Biology Program in Drug Discovery, Department of Pharmacology, Vanderbilt Medical Center, Nashville, Tennessee 37240, United States
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3
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Oh KK, Yoon SJ, Song SH, Park JH, Kim JS, Kim MJ, Kwon GH, Kim DJ, Suk KT. The interdisciplinary approach to investigate bona fide agent(s) in flavonoids or alkaloids in treating HCC. ARTIFICIAL CELLS, NANOMEDICINE, AND BIOTECHNOLOGY 2024; 52:500-511. [PMID: 39387711 DOI: 10.1080/21691401.2024.2413536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 08/30/2024] [Accepted: 09/26/2024] [Indexed: 10/15/2024]
Abstract
Currently, the treatment of hepatocellular carcinoma (HCC) is yet to be determined, alternatively, flavonoids or alkaloids from nature have been considered as significant mediators against HCC. In the scenario, we pioneered the most significant agent(s) in either flavonoid(s) or alkaloid(s) against HCC with cheminformatics, bioinformatics, computer screening tools and quantum chemistry concept. In prospect, the intent was to provide the theoretical scaffold in the myriad natural organic molecules. The cheminformatics (natural product activity & species source database (NPASS), SwissADME, PubChem, Similarity Ensemble Approach (SEA) and SwissTargetPrediction (STP)), bioinformatics (DisGeNET, OMIM and STRING) were employed to underpin promising therapeutic components. The protein-protein interaction (PPI) network to identify the relationships between each target and a bubble chart to elucidate key signalling pathway(s) was constructed via STRING database. Ultimately, computer screening tools (PyMOL and AutoDockTools 1.5.6) and quantum chemistry (GaussView 6 and Gaussian) concept were adopted to decrypt the key molecule(s), target(s) and key mechanism(s). The most significant target was AKT1 in PPI network, AKT1 - isorhamnetin, MCL1 - ochrindole D and PIM1 - heyneanine hydroxyindolenine were the most stable conformers to antagonize JAK-STAT signalling pathway. This study provides scientific manifestation to facilitate the clinical test despite the enormous complexity of herbal medicine, and the devised platform for further clarifying the bioactive(s) and mechanism(s) against HCC.
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Affiliation(s)
- Ki-Kwang Oh
- College of Medicine, Institute for Liver and Digestive Diseases, Hallym University, Chuncheon, South Korea
| | - Sang-Jun Yoon
- College of Medicine, Institute for Liver and Digestive Diseases, Hallym University, Chuncheon, South Korea
| | - Seol Hee Song
- College of Medicine, Institute for Liver and Digestive Diseases, Hallym University, Chuncheon, South Korea
| | - Jeong Ha Park
- College of Medicine, Institute for Liver and Digestive Diseases, Hallym University, Chuncheon, South Korea
| | - Jeong Su Kim
- College of Medicine, Institute for Liver and Digestive Diseases, Hallym University, Chuncheon, South Korea
| | - Min Ju Kim
- College of Medicine, Institute for Liver and Digestive Diseases, Hallym University, Chuncheon, South Korea
| | - Goo-Hyun Kwon
- College of Medicine, Institute for Liver and Digestive Diseases, Hallym University, Chuncheon, South Korea
| | - Dong Joon Kim
- College of Medicine, Institute for Liver and Digestive Diseases, Hallym University, Chuncheon, South Korea
| | - Ki-Tae Suk
- College of Medicine, Institute for Liver and Digestive Diseases, Hallym University, Chuncheon, South Korea
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4
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Noor F, Junaid M, Almalki AH, Almaghrabi M, Ghazanfar S, Tahir Ul Qamar M. Deep learning pipeline for accelerating virtual screening in drug discovery. Sci Rep 2024; 14:28321. [PMID: 39550439 PMCID: PMC11569207 DOI: 10.1038/s41598-024-79799-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Accepted: 11/12/2024] [Indexed: 11/18/2024] Open
Abstract
In the race to combat ever-evolving diseases, the drug discovery process often faces the hurdles of high-cost and time-consuming procedures. To tackle these challenges and enhance the efficiency of identifying new therapeutic agents, we introduce VirtuDockDL, which is a streamlined Python-based web platform utilizing deep learning for drug discovery. This pipeline employs a Graph Neural Network to analyze and predict the effectiveness of various compounds as potential drug candidates. During the validation phase, VirtuDockDL was instrumental in identifying non-covalent inhibitors against the VP35 protein of the Marburg virus, a critical target given the virus's high fatality rate and limited treatment options. Further, in benchmarking, VirtuDockDL achieved 99% accuracy, an F1 score of 0.992, and an AUC of 0.99 on the HER2 dataset, surpassing DeepChem (89% accuracy) and AutoDock Vina (82% accuracy). Compared to RosettaVS, MzDOCK, and PyRMD, VirtuDockDL outperformed them by combining both ligand- and structure-based screening with deep learning. While RosettaVS excels in accurate docking but lacks high-throughput screening, and PyRMD focuses on ligand-based methods without AI integration, VirtuDockDL offers superior predictive accuracy and full automation for large-scale datasets, making it ideal for comprehensive drug discovery workflows. These results underscore the tool's capability to identify high-affinity inhibitors accurately across various targets, including the HER2 protein for cancer therapy, TEM-1 beta-lactamase for bacterial infections, and the CYP51 enzyme for fungal infections like Candidiasis. To sum up, VirtuDockDL combines user-friendly interface design with powerful computational capabilities to facilitate rapid, cost-effective drug discovery and development. The integration of AI in drug discovery could potentially transform the landscape of pharmaceutical research, providing faster responses to global health challenges. The VirtuDockDL is available at https://github.com/FatimaNoor74/VirtuDockDL .
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Affiliation(s)
- Fatima Noor
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, 35000, Pakistan
- Integrative Omics and Molecular Modeling Laboratory, Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad, 38000, Pakistan
| | - Muhammad Junaid
- Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
| | - Atiah H Almalki
- Department of Pharmaceutical Chemistry, College of Pharmacy, Taif University, P.O. Box 11099, 21944, Taif, Saudi Arabia
- Addiction and Neuroscience Research Unit, College of Pharmacy, Taif University, Al-Hawiah, 21944, Taif, Saudi Arabia
| | - Mohammed Almaghrabi
- Pharmacognosy and Pharmaceutical Chemistry Department, Faculty of Pharmacy, Taibah University, 30001, Al Madinah Al Munawarah, Saudi Arabia
| | - Shakira Ghazanfar
- National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Center (NARC), Islamabad, Pakistan
| | - Muhammad Tahir Ul Qamar
- Integrative Omics and Molecular Modeling Laboratory, Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad, 38000, Pakistan.
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5
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Ojuka P, Ochieng CO, Ndarawit W, Nyongesa DW, Mukavi J, Nyabuga Nyariki J, Apollo S, Santos CBR, Kimani NM. Alkaloids Isolated from Vepris glandulosa with Antidiabetic Properties: An In Vitro and In Silico Analysis. Chem Biodivers 2024:e202401515. [PMID: 39495611 DOI: 10.1002/cbdv.202401515] [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: 06/23/2024] [Revised: 10/22/2024] [Accepted: 11/04/2024] [Indexed: 11/06/2024]
Abstract
Diabetes is a major global health issue and as current treatments fail, the search for new antidiabetic drugs is crucial. This investigation, focusing on identifying potential antidiabetic compounds from the endangered plant species Vepris glandulosa, led to the isolation of two known alkaloids, choisyine acetate (1) and choisyine (2). The study established the in vitro inhibitory activities and in silico molecular interaction of the two alkaloids with α-amylase based on IC50 values, Linewaever-Burk/Dixon plot kinetic analyses and Molecular docking, respectively. The α-amylase inhibition assay revealed noncompetitive inhibition for both compounds with IC50 and Ki values of 4.74±0.17 and 4.75 mM for compound 1, and 11.29±0.44 and 12.37 mM for compound 2, respectively. In comparison, the standard drug acarbose displayed a competitive mode of inhibition, with IC50 and Ki values of 11.99±0.02 and 12.68 mM, respectively. The binding affinities with α-amylase were -6.42 and -6.07 kcal/mol for compounds 1 and 2, respectively relative to acarbose -8.03 Kcal/mol. Moreover, these two compounds' predicted physicochemical and ADMET properties justified their potential as lead compounds for drug discovery. These compounds demonstrated remarkable inhibition potential comparable to the standard drug, highlighting their potential as viable alternatives in managing diabetes.
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Affiliation(s)
- Prince Ojuka
- Department of Physical Science, University of Embu, P.O Box 6-60100, Embu, Kenya
| | - Charles O Ochieng
- Department of Chemistry, Maseno University, Private Bag, Maseno, Kenya
| | - Wilberforce Ndarawit
- Department of Physical Science, University of Embu, P.O Box 6-60100, Embu, Kenya
| | - Daniel W Nyongesa
- Department of Chemistry, Maseno University, Private Bag, Maseno, Kenya
| | - Justus Mukavi
- Institute of Pharmaceutical Biology and Phytochemistry (IPBP), University of Münster, PharmaCampus Corrensstrasse 48, Muenster, D-48149, Germany
| | - James Nyabuga Nyariki
- Department of Biochemistry and Biotechnology, Technical of University of Kenya, P.O Box 52428-00200, Nairobi, Kenya
| | - Seth Apollo
- Department of Physical Science, University of Embu, P.O Box 6-60100, Embu, Kenya
| | - Cleydson B R Santos
- Laboratory of Modeling and Computational Chemistry, Department of Biological Sciences and Health, Federal University of Amapá, Macapá, Amapá, Brazil
- Graduate Program in Medicinal Chemistry and Molecular Modelling, Health Science Institute, Federal University of Pará, 66075-110, Belém, PA, Brazil
| | - Njogu M Kimani
- Department of Physical Science, University of Embu, P.O Box 6-60100, Embu, Kenya
- Natural Product Chemistry and Computational Drug Discovery Laboratory, Embu, Kenya
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6
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Indalkar S, Kumar Sahoo D, Bhange DS, Waghmode M, Shekh S, Gaikwad LD, Gadave KM. Pyrimidine-based sulfonamides and acetamides as potent antimicrobial Agents: Synthesis, Computational Studies, and biological assessment. Bioorg Chem 2024; 151:107667. [PMID: 39067418 DOI: 10.1016/j.bioorg.2024.107667] [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: 04/15/2024] [Revised: 07/09/2024] [Accepted: 07/21/2024] [Indexed: 07/30/2024]
Abstract
A series of novel sulfonamide and acetamide derivatives of pyrimidine were synthesized and their antimicrobial activities were assessed. Based on the Microbroth dilution method, the minimum inhibitory concentration (MIC) of the synthesized compounds demonstrated moderate to good levels of antifungal and antibacterial activity. Structure-activity relationship analysis suggested that the presence of electron-withdrawing groups, such as halogens, nitrile, and nitro groups, on the pyrimidine ring contributed to the enhanced antimicrobial potency, while electron-donating substituents led to a decrease in activity. Computational studies, including density functional theory (DFT), frontier molecular orbitals (FMO), and molecular electrostatic potential (MEP) analysis, provided insights into the electronic properties and charge distribution of the compounds. Drug-likeness evaluation using ADME/Tox analysis indicated that the synthesized compounds possess favorable physicochemical properties and could be potential drug candidates. Molecular docking against the Mycobacterium TB protein tyrosine phosphatase B (MtbPtpB) revealed that the synthesized compounds exhibited strong binding affinities (-46 kcal/mol to - 61 kcal/mol) and formed stable protein-ligand complexes through hydrogen bonding and π-π stacking interactions with key residues in the active site. The observed interactions from the docking simulations were consistent with the predicted interaction sites identified in the FMO and MEP analyses. These findings suggest that the synthesized pyrimidine derivatives could serve as promising antimicrobial agents and warrant further investigation for drug development.
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Affiliation(s)
- Supriya Indalkar
- Department of Chemistry Prof. Ramakrishna Arts Commerce and Science College, Savitribai Phule Pune University, India; Department of Chemistry, Dr. D.Y. Patil Arts, Commerce & Science College, Pimpri, Savitribai Phule Pune University, India.
| | - Dipak Kumar Sahoo
- School of Sciences, Woxsen University, Kamkole, Sadasivpet, Sangareddy District, Hyderabad 502345, Telangana, India.
| | - Dattatraya S Bhange
- Department of Chemistry Prof. Ramakrishna Arts Commerce and Science College, Savitribai Phule Pune University, India
| | | | - Shamasoddin Shekh
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Lalaso D Gaikwad
- School of Chemical Sciences, Swami Ramanand Teerth Marathwada University, Nanded, India
| | - Kisan M Gadave
- Annasaheb Magar College, Savitribai, Phule Pune University, India.
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7
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Fernandes GFS, Kim SH, Castagnolo D. Harnessing biocatalysis as a green tool in antibiotic synthesis and discovery. RSC Adv 2024; 14:30396-30410. [PMID: 39318457 PMCID: PMC11420778 DOI: 10.1039/d4ra04824e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Accepted: 09/16/2024] [Indexed: 09/26/2024] Open
Abstract
Biocatalysis offers a sustainable approach to drug synthesis, leveraging the high selectivity and efficiency of enzymes. This review explores the application of biocatalysis in the early-stage synthesis of antimicrobial compounds, emphasizing its advantages over traditional chemical methods. We discuss various biocatalysts, including enzymes and whole-cell systems, and their role in the selective functionalization and preparation of antimicrobials and antibacterial building blocks. The review underscores the potential of biocatalysis to advance the development of new antibiotics and suggests directions and potential applications of enzymes in drug development.
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Affiliation(s)
- Guilherme F S Fernandes
- Department of Chemistry, University College London 20 Gordon Street London WC1H 0AJ UK
- School of Pharmacy, University College London 29-39 Brunswick Square London WC1N 1AX UK
| | - Seong-Heun Kim
- Institute of Pharmaceutical Science, School of Cancer & Pharmaceutical Science, King's College London 150 Stamford Street London SE1 9NH UK
| | - Daniele Castagnolo
- Department of Chemistry, University College London 20 Gordon Street London WC1H 0AJ UK
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8
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Holder L, Yuce E, Oriomah G, Jenkins AP, Reynisson J, Winter A, Cosgrove SC. Accessing Active Fragments for Drug Discovery Utilising Nitroreductase Biocatalysis. Chembiochem 2024; 25:e202400428. [PMID: 38940076 DOI: 10.1002/cbic.202400428] [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: 05/14/2024] [Revised: 06/26/2024] [Accepted: 06/27/2024] [Indexed: 06/29/2024]
Abstract
Biocatalysis has played a limited role in the early stages of drug discovery. This is often attributed to the limited substrate scope of enzymes not affording access to vast areas of novel chemical space. Here, we have shown a promiscuous nitroreductase enzyme (NR-55) can be used to produce a panel of functionalised anilines from a diverse panel of aryl nitro starting materials. After screening on analytical scale, we show that sixteen substrates could be scaled to 1 mmol scale, with several poly-functional anilines afforded with ease under the standard conditions. The aniline products were also screened for activity against several cell lines of interest, with modest activity observed for one compound. This study demonstrates the potential for nitroreductase biocatalysis to provide access to functional fragments under benign conditions.
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Affiliation(s)
- Lauren Holder
- School of Chemical and Physical Sciences & Centre for Glycoscience, Keele University, Keele, Staffordshire, ST5 5BG, United Kingdom
| | - Eda Yuce
- School of Life Sciences, Keele University, Keele, Staffordshire, ST5 5BG, United Kingdom
| | - Gabriel Oriomah
- School of Life Sciences, Keele University, Keele, Staffordshire, ST5 5BG, United Kingdom
| | - Aimee-Page Jenkins
- School of Chemical and Physical Sciences & Centre for Glycoscience, Keele University, Keele, Staffordshire, ST5 5BG, United Kingdom
| | - Jóhannes Reynisson
- School of Life Sciences, Keele University, Keele, Staffordshire, ST5 5BG, United Kingdom
- School of Pharmacy, Keele University, Keele, Staffordshire, ST5 5BG, United Kingdom
| | - Anja Winter
- School of Life Sciences, Keele University, Keele, Staffordshire, ST5 5BG, United Kingdom
| | - Sebastian C Cosgrove
- School of Chemical and Physical Sciences & Centre for Glycoscience, Keele University, Keele, Staffordshire, ST5 5BG, United Kingdom
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Hollmann F, Sanchis J, Reetz MT. Learning from Protein Engineering by Deconvolution of Multi-Mutational Variants. Angew Chem Int Ed Engl 2024; 63:e202404880. [PMID: 38884594 DOI: 10.1002/anie.202404880] [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: 03/11/2024] [Revised: 06/05/2024] [Accepted: 06/06/2024] [Indexed: 06/18/2024]
Abstract
This review analyzes a development in biochemistry, enzymology and biotechnology that originally came as a surprise. Following the establishment of directed evolution of stereoselective enzymes in organic chemistry, the concept of partial or complete deconvolution of selective multi-mutational variants was introduced. Early deconvolution experiments of stereoselective variants led to the finding that mutations can interact cooperatively or antagonistically with one another, not just additively. During the past decade, this phenomenon was shown to be general. In some studies, molecular dynamics (MD) and quantum mechanics/molecular mechanics (QM/MM) computations were performed in order to shed light on the origin of non-additivity at all stages of an evolutionary upward climb. Data of complete deconvolution can be used to construct unique multi-dimensional rugged fitness pathway landscapes, which provide mechanistic insights different from traditional fitness landscapes. Along a related line, biochemists have long tested the result of introducing two point mutations in an enzyme for mechanistic reasons, followed by a comparison of the respective double mutant in so-called double mutant cycles, which originally showed only additive effects, but more recently also uncovered cooperative and antagonistic non-additive effects. We conclude with suggestions for future work, and call for a unified overall picture of non-additivity and epistasis.
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Affiliation(s)
- Frank Hollmann
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629HZ, Delft, Netherlands
| | - Joaquin Sanchis
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, 3052, Australia
| | - Manfred T Reetz
- Max-Plank-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45481, Mülheim, Germany
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
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10
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Puls K, Olivé-Marti AL, Hongnak S, Lamp D, Spetea M, Wolber G. Discovery of Novel, Selective, and Nonbasic Agonists for the Kappa-Opioid Receptor Determined by Salvinorin A-Based Virtual Screening. J Med Chem 2024; 67:13788-13801. [PMID: 39088801 PMCID: PMC11345774 DOI: 10.1021/acs.jmedchem.4c00590] [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: 03/11/2024] [Revised: 07/12/2024] [Accepted: 07/19/2024] [Indexed: 08/03/2024]
Abstract
Modulating the kappa-opioid receptor (KOR) is a promising strategy for treating various human diseases. KOR agonists show potential for treating pain, pruritus, and epilepsy, while KOR antagonists show potential for treating depression, anxiety, and addiction. The diterpenoid Salvinorin A (SalA), a secondary metabolite of Salvia divinorum, is a potent and selective KOR agonist. Unlike typical opioids, SalA lacks a basic nitrogen, which encouraged us to search for nonbasic KOR ligands. Through structure-based virtual screening using 3D pharmacophore models based on the binding mode of SalA, we identified novel, nonbasic, potent, and selective KOR agonists. In vitro studies confirmed two virtual hits, SalA-VS-07 and SalA-VS-08, as highly selective for the KOR and showing G protein-biased KOR agonist activity. Both KOR ligands share a novel spiro-moiety and a nonbasic scaffold. Our findings provide novel starting points for developing therapeutics aimed at treating pain and other conditions in which KOR is a central player.
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Affiliation(s)
- Kristina Puls
- Department
of Pharmaceutical Chemistry, Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Str. 2-4, 14195 Berlin, Germany
| | - Aina-Leonor Olivé-Marti
- Department
of Pharmaceutical Chemistry, Institute of Pharmacy and Center for
Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Siriwat Hongnak
- Department
of Pharmaceutical Chemistry, Institute of Pharmacy and Center for
Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - David Lamp
- Department
of Pharmaceutical Chemistry, Institute of Pharmacy and Center for
Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Mariana Spetea
- Department
of Pharmaceutical Chemistry, Institute of Pharmacy and Center for
Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Gerhard Wolber
- Department
of Pharmaceutical Chemistry, Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Str. 2-4, 14195 Berlin, Germany
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11
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Heinzke AL, Pahl A, Zdrazil B, Leach AR, Waldmann H, Young RJ, Leeson PD. Occurrence of "Natural Selection" in Successful Small Molecule Drug Discovery. J Med Chem 2024; 67:11226-11241. [PMID: 38949112 PMCID: PMC11247505 DOI: 10.1021/acs.jmedchem.4c00811] [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: 04/05/2024] [Revised: 06/08/2024] [Accepted: 06/13/2024] [Indexed: 07/02/2024]
Abstract
Published compounds from ChEMBL version 32 are used to seek evidence for the occurrence of "natural selection" in drug discovery. Three measures of natural product (NP) character were applied, to compare time- and target-matched compounds reaching the clinic (clinical compounds in phase 1-3 development and approved drugs) with background compounds (reference compounds). Pseudo-NPs (PNPs), containing NP fragments combined in ways inaccessible by nature, are increasing over time, reaching 67% of clinical compounds first disclosed since 2010. PNPs are 54% more likely to be found in post-2008 clinical versus reference compounds. The majority of target classes show increased clinical compound NP character versus their reference compounds. Only 176 NP fragments appear in >1000 clinical compounds published since 2008, yet these make up on average 63% of the clinical compound's core scaffolds. There is untapped potential awaiting exploitation, by applying nature's building blocks─"natural intelligence"─to drug design.
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Affiliation(s)
- A. Lina Heinzke
- European
Molecular Biology Laboratory, European Bioinformatics
Institute, Wellcome Genome Campus, Hinxton CB10 1SD, Cambridgeshire, U.K.
| | - Axel Pahl
- Compound
Management and Screening Center, Max-Planck-Institute
of Molecular Physiology, Otto-Hahn-Straße 11, 44227 Dortmund, Germany
| | - Barbara Zdrazil
- European
Molecular Biology Laboratory, European Bioinformatics
Institute, Wellcome Genome Campus, Hinxton CB10 1SD, Cambridgeshire, U.K.
| | - Andrew R. Leach
- European
Molecular Biology Laboratory, European Bioinformatics
Institute, Wellcome Genome Campus, Hinxton CB10 1SD, Cambridgeshire, U.K.
| | - Herbert Waldmann
- Department
of Chemical Biology, Max-Planck-Institute
of Molecular Physiology, Otto-Hahn-Straße 11, 44227 Dortmund, Germany
- Faculty
of Chemistry and Chemical Biology, Technical
University Dortmund, Otto-Hahn-Straße 6, 44227 Dortmund, Germany
| | | | - Paul D. Leeson
- Paul Leeson
Consulting Ltd., Nuneaton CV13 6LZ, Warwickshire, U.K.
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12
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Lescano LE, Salazar MO, Furlan RLE. Chemically engineered essential oils prepared through thiocyanation under solvent-free conditions: chemical and bioactivity alteration. NATURAL PRODUCTS AND BIOPROSPECTING 2024; 14:35. [PMID: 38822174 PMCID: PMC11143095 DOI: 10.1007/s13659-024-00456-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 05/17/2024] [Indexed: 06/02/2024]
Abstract
The generation of chemically engineered essential oils (CEEOs) prepared from bi-heteroatomic reactions using ammonium thiocyanate as a source of bioactive compounds is described. The impact of the reaction on the chemical composition of the mixtures was qualitatively demonstrated through GC-MS, utilizing univariate and multivariate analysis. The reaction transformed most of the components in the natural mixtures, thereby expanding the chemical diversity of the mixtures. Changes in inhibition properties between natural and CEEOs were demonstrated through acetylcholinesterase TLC autography, resulting in a threefold increase in the number of positive events due to the modification process. The chemically engineered Origanum vulgare L. essential oil was subjected to bioguided fractionation, leading to the discovery of four new active compounds with similar or higher potency than eserine against the enzyme. The results suggest that the directed chemical transformation of essential oils can be a valuable strategy for discovering new acetylcholinesterase (AChE) inhibitors.
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Affiliation(s)
- Liz E Lescano
- Farmacognosia, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Suipacha 531, 2000, Rosario, Argentina
| | - Mario O Salazar
- Farmacognosia, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Suipacha 531, 2000, Rosario, Argentina.
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Suipacha 531, 2000, Rosario, Argentina.
| | - Ricardo L E Furlan
- Farmacognosia, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), Suipacha 531, 2000, Rosario, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Suipacha 531, 2000, Rosario, Argentina
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13
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Denner TC, Heise NV, Hoenke S, Csuk R. Synthesis of Rhodamine-Conjugated Lupane Type Triterpenes of Enhanced Cytotoxicity. Molecules 2024; 29:2346. [PMID: 38792206 PMCID: PMC11123818 DOI: 10.3390/molecules29102346] [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: 04/17/2024] [Revised: 05/06/2024] [Accepted: 05/15/2024] [Indexed: 05/26/2024] Open
Abstract
Various conjugates with rhodamines were prepared by starting with betulinic acid (BA) and platanic acid (PA). The molecules homopiperazine and piperazine, which were identified in earlier research, served as linkers between the rhodamine and the triterpene. The pentacyclic triterpene's ring A was modified with two acetyloxy groups in order to possibly boost its cytotoxic activity. The SRB assays' cytotoxicity data showed that conjugates 13-22, derived from betulinic acid, had a significantly higher cytotoxicity. Of these hybrids, derivatives 19 (containing rhodamine B) and 22 (containing rhodamine 101) showed the best values with EC50 = 0.016 and 0.019 μM for A2780 ovarian carcinoma cells. Additionally, based on the ratio of EC50 values, these two compounds demonstrated the strongest selectivity between malignant A2780 cells and non-malignant NIH 3T3 fibroblasts. A375 melanoma cells were used in cell cycle investigations, which showed that the cells were halted in the G1/G0 phase. Annexin V/FITC/PI staining demonstrated that the tumor cells were affected by both necrosis and apoptosis.
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Affiliation(s)
| | | | | | - René Csuk
- Organic Chemistry, Martin-Luther University Halle-Wittenberg, Kurt-Mothes, Str. 2, 06120 Halle (Saale), Germany
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14
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Zhou TP, Feng J, Wang Y, Li S, Wang B. Substrate Conformational Switch Enables the Stereoselective Dimerization in P450 NascB: Insights from Molecular Dynamics Simulations and Quantum Mechanical/Molecular Mechanical Calculations. JACS AU 2024; 4:1591-1604. [PMID: 38665654 PMCID: PMC11040706 DOI: 10.1021/jacsau.4c00075] [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: 01/23/2024] [Revised: 03/20/2024] [Accepted: 03/21/2024] [Indexed: 04/28/2024]
Abstract
P450 NascB catalyzes the coupling of cyclo-(l-tryptophan-l-proline) (1) to generate (-)-naseseazine C (2) through intramolecular C-N bond formation and intermolecular C-C coupling. A thorough understanding of its catalytic mechanism is crucial for the engineering or design of P450-catalyzed C-N dimerization reactions. By employing MD simulations, QM/MM calculations, and enhanced sampling, we assessed various mechanisms from recent works. Our study demonstrates that the most favorable pathway entails the transfer of a hydrogen atom from N7-H to Cpd I. Subsequently, there is a conformational change in the substrate radical, shifting it from the Re-face to the Si-face of N7 in Substrate 1. The Si-face conformation of Substrate 1 is stabilized by the protein environment and the π-π stacking interaction between the indole ring and heme porphyrin. The subsequent intermolecular C3-C6' bond formation between Substrate 1 radical and Substrate 2 occurs via a radical attack mechanism. The conformational switch of the Substrate 1 radical not only lowers the barrier of the intermolecular C3-C6' bond formation but also yields the correct stereoselectivity observed in experiments. In addition, we evaluated the reactivity of the ferric-superoxide species, showing it is not reactive enough to initiate the hydrogen atom abstraction from the indole NH group of the substrate. Our simulation provides a comprehensive mechanistic insight into how the P450 enzyme precisely controls both the intramolecular C-N cyclization and intermolecular C-C coupling. The current findings align with the available experimental data, emphasizing the pivotal role of substrate dynamics in governing P450 catalysis.
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Affiliation(s)
- Tai-Ping Zhou
- State
Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian
Provincial Key Laboratory of Theoretical and Computational Chemistry,
College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Jianqiang Feng
- State
Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian
Provincial Key Laboratory of Theoretical and Computational Chemistry,
College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Yongchao Wang
- State
Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian
Provincial Key Laboratory of Theoretical and Computational Chemistry,
College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Shengying Li
- State
Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Binju Wang
- State
Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian
Provincial Key Laboratory of Theoretical and Computational Chemistry,
College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
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15
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Kibet S, Kimani NM, Mwanza SS, Mudalungu CM, Santos CBR, Tanga CM. Unveiling the Potential of Ent-Kaurane Diterpenoids: Multifaceted Natural Products for Drug Discovery. Pharmaceuticals (Basel) 2024; 17:510. [PMID: 38675469 PMCID: PMC11054903 DOI: 10.3390/ph17040510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 03/29/2024] [Accepted: 04/02/2024] [Indexed: 04/28/2024] Open
Abstract
Natural products hold immense potential for drug discovery, yet many remain unexplored in vast libraries and databases. In an attempt to fill this gap and meet the growing demand for effective drugs, this study delves into the promising world of ent-kaurane diterpenoids, a class of natural products with huge therapeutic potential. With a dataset of 570 ent-kaurane diterpenoids obtained from the literature, we conducted an in silico analysis, evaluating their physicochemical, pharmacokinetic, and toxicological properties with a focus on their therapeutic implications. Notably, these natural compounds exhibit drug-like properties, aligning closely with those of FDA-approved drugs, indicating a high potential for drug development. The ranges of the physicochemical parameters were as follows: molecular weights-288.47 to 626.82 g/mol; number of heavy atoms-21 to 44; the number of hydrogen bond donors and acceptors-0 to 8 and 1 to 11, respectively; the number of rotatable bonds-0 to 11; fraction Csp3-0.65 to 1; and TPSA-20.23 to 189.53 Ų. Additionally, the majority of these molecules display favorable safety profiles, with only 0.70%, 1.40%, 0.70%, and 46.49% exhibiting mutagenic, tumorigenic, reproduction-enhancing, and irritant properties, respectively. Importantly, ent-kaurane diterpenoids exhibit promising biopharmaceutical properties. Their average lipophilicity is optimal for drug absorption, while over 99% are water-soluble, facilitating delivery. Further, 96.5% and 28.20% of these molecules exhibited intestinal and brain bioavailability, expanding their therapeutic reach. The predicted pharmacological activities of these compounds encompass a diverse range, including anticancer, immunosuppressant, chemoprotective, anti-hepatic, hepatoprotectant, anti-inflammation, antihyperthyroidism, and anti-hepatitis activities. This multi-targeted profile highlights ent-kaurane diterpenoids as highly promising candidates for further drug discovery endeavors.
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Affiliation(s)
- Shadrack Kibet
- Department of Physical Sciences, University of Embu, Embu P.O. Box 6-60100, Kenya; (S.K.); (S.S.M.)
- International Centre of Insects Physiology and Ecology, Nairobi P.O. Box 30772-00100, Kenya;
| | - Njogu M. Kimani
- Department of Physical Sciences, University of Embu, Embu P.O. Box 6-60100, Kenya; (S.K.); (S.S.M.)
- Natural Product Chemistry and Computational Drug Discovery Laboratory, Embu P.O. Box 6-60100, Kenya
| | - Syombua S. Mwanza
- Department of Physical Sciences, University of Embu, Embu P.O. Box 6-60100, Kenya; (S.K.); (S.S.M.)
- International Centre of Insects Physiology and Ecology, Nairobi P.O. Box 30772-00100, Kenya;
| | - Cynthia M. Mudalungu
- International Centre of Insects Physiology and Ecology, Nairobi P.O. Box 30772-00100, Kenya;
- School of Chemistry and Material Science, The Technical University of Kenya, Nairobi P.O. Box 52428-00200, Kenya
| | - Cleydson B. R. Santos
- Graduate Program in Medicinal Chemistry and Molecular Modelling, Health Science Institute, Federal University of Pará, Belém 66075-110, Brazil;
- Laboratory of Modelling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, Brazil
| | - Chrysantus M. Tanga
- International Centre of Insects Physiology and Ecology, Nairobi P.O. Box 30772-00100, Kenya;
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16
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Tang J, Su L, He X, Liu D, Zhao C, Zhang S, Li Q, Li R, Li H. Biotransformation of Patchouli Alcohol by Cladosporium cladosporioides and the Anti-Influenza Virus Activities of Biotransformation Products. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:7991-8005. [PMID: 38544458 DOI: 10.1021/acs.jafc.3c09753] [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: 04/11/2024]
Abstract
The biotransformation of patchouli alcohol by Cladosporium cladosporioides afforded 31 products, including 21 new ones (1-3, 5, 6, 8-14, and 17-25). Their structures were determined by extensive spectroscopic data analysis (1H and 13C NMR, HSQC, HMBC, 1H-1H COSY, ROESY, and HRESIMS), and the absolute configuration of compounds 1, 2, 8, 9, and 17 was determined by single-crystal X-ray diffraction using Cu Kα radiation. Structurally, compounds 21-24 were patchoulol-type norsesquiterpenoids without Me-12. Among them, a Δ3(4) double bond existed in compounds 21 and 22; a three-membered ring was formed between C-4, C-5, and C-6 in compound 23; an epoxy moiety appeared between C-3 and C-4 in compound 24. Furthermore, the biotransformation products 9, 10, 12, and 25 showed potent anti-influenza virus activity with EC50 values of 2.11, 7.94, 20.87, and 3.45 μM, respectively.
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Affiliation(s)
- Jianxian Tang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, P.R. China
| | - Lu Su
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, P.R. China
| | - Xiu He
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, P.R. China
| | - Dan Liu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, P.R. China
| | - Chunyan Zhao
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, P.R. China
| | - Shixian Zhang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, P.R. China
| | - Qin Li
- School of Basic Medical Sciences, Yunnan University of Chinese Medicine, Kunming 650500, P.R. China
| | - Rongtao Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, P.R. China
| | - Hongmei Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, P.R. China
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17
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Shenvi RA. Natural Product Synthesis in the 21st Century: Beyond the Mountain Top. ACS CENTRAL SCIENCE 2024; 10:519-528. [PMID: 38559299 PMCID: PMC10979479 DOI: 10.1021/acscentsci.3c01518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 01/08/2024] [Accepted: 01/09/2024] [Indexed: 04/04/2024]
Abstract
Research into natural products emerged from humanity's curiosity about the nature of matter and its role in the materia medica of diverse civilizations. Plants and fungi, in particular, supplied materials that altered behavior, perception, and well-being profoundly. Many active principles remain well-known today: strychnine, morphine, psilocybin, ephedrine. The potential to circumvent the constraints of natural supply and explore the properties of these materials led to the field of natural product synthesis. This research delivered new molecules with new properties, but also led to fundamental insights into the chemistry of the nonmetal elements H, C, N, O, P, S, Se, and their combinations, i.e., organic chemistry. It also led to a potent culture focused on bigger molecules and races to the finish line, perhaps at the expense of actionable next steps. About 20 years ago, the field began to contract in the United States. Research that focused solely on chemical reaction development, especially catalysis, filled the void. After all, new reactions and mechanistic insight could be immediately implemented by the chemistry community, so it became hard to justify the lengthy procurement of a complex molecule that sat in the freezer unused. This shift coincided with a divestment of natural product portfolios by pharmaceutical companies and an emphasis in academic organic chemistry on applications-driven research, perhaps at the expense of more fundamental science. However, as bioassays and the tools of chemical biology become widespread, synthesis finds a new and powerful ally that allows us to better deliver on the premise of the field. And the hard-won insights of complex synthesis can be better encoded digitally, mined by data science, and applied to new challenges, as chemists perturb and even surpass the properties of complex natural products. The 21st century promises powerful developments, both in fundamental organic chemistry and at the interface of synthesis and biology, if the community of scientists fosters its growth. This essay tries to contextualize natural product synthesis for a broad audience, looks ahead to its transformation in the coming years, and expects the future to be bright.
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Affiliation(s)
- Ryan A. Shenvi
- Department
of Chemistry, Scripps Research, La Jolla, California 92037, United States
- Graduate
School of Chemical and Biological Sciences, Scripps Research, La Jolla, California 92037, United States
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18
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Suckling CJ. The allure of targets for novel drugs. RSC Med Chem 2024; 15:472-484. [PMID: 38389887 PMCID: PMC10880906 DOI: 10.1039/d3md00621b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 12/12/2023] [Indexed: 02/24/2024] Open
Abstract
The challenges of bringing new medicines to patients have been extensively discussed and debated, including consideration of the contribution that academic laboratories can make. At the University of Strathclyde, drug discovery has been a continuing focal activity since the 1960s, and in the past 30 years, the author has led or contributed to many projects of different character and for diverse diseases. A feature common to these projects is the extension of concepts of molecular and biological targets in drug discovery research. In mechanistic terms, these have included compounds that are activators and not inhibitors, and in particular multitargeted compounds. With respect to relevance to disease, schizophrenia, pulmonary disfunction, autoimmune, and infectious disease are most relevant. These projects are discussed in the context of classical medicinal chemistry and more recent concepts in and approaches to drug discovery.
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Affiliation(s)
- Colin J Suckling
- Department of Pure & Applied Chemistry, University of Strathclyde 295 Cathedral Street Glasgow G1 1Xl Scotland UK
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19
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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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20
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Angelini E, Martinelli M, Roà E, Ungarean CN, Salome C, Lefebvre Q, Bournez C, Fessard TC, Sarlah D. Diversification of Simple Arenes into Complex (Amino)cyclitols. Chemistry 2024; 30:e202303262. [PMID: 37856371 DOI: 10.1002/chem.202303262] [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: 10/10/2023] [Revised: 10/17/2023] [Accepted: 10/18/2023] [Indexed: 10/21/2023]
Abstract
Highly oxygenated cyclohexanes, including (amino)cyclitols, are featured in natural products possessing a notable range of biological activities. As such, these building blocks are valuable tools for medicinal chemistry. While de novo synthetic strategies have provided access to select compounds, challenges including stereochemical density and complexity have hindered the development of a general approach to (amino)cyclitol structures. This work reports the use of arenophile chemistry to access dearomatized intermediates which are amenable to diverse downstream transformations. Practical guidelines were developed for the synthesis of natural and non-natural (amino)cyclitols from simple arenes through a series of strategic functionalization events.
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Affiliation(s)
- Elisa Angelini
- Department of Chemistry, University of Pavia, Viale Taramelli 12, 27100, Pavia, Italy
| | - Matteo Martinelli
- Department of Chemistry, University of Pavia, Viale Taramelli 12, 27100, Pavia, Italy
| | - Eugenio Roà
- Department of Chemistry, University of Pavia, Viale Taramelli 12, 27100, Pavia, Italy
| | - Chad N Ungarean
- Department of Chemistry, University of Pavia, Viale Taramelli 12, 27100, Pavia, Italy
| | | | | | - Colin Bournez
- SpiroChem AG, Mattenstrasse 22, 4058, Basel, Switzerland
| | | | - David Sarlah
- Department of Chemistry, University of Pavia, Viale Taramelli 12, 27100, Pavia, Italy
- Department of Chemistry, Carl R. Woese Institute for Genomic Biology, Cancer Center at Illinois, University of Illinois, 61801, Urbana, Illinois, USA
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21
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Mikutis S, Lawrinowitz S, Kretzer C, Dunsmore L, Sketeris L, Rodrigues T, Werz O, Bernardes GJL. Machine Learning Uncovers Natural Product Modulators of the 5-Lipoxygenase Pathway and Facilitates the Elucidation of Their Biological Mechanisms. ACS Chem Biol 2024; 19:217-229. [PMID: 38149598 PMCID: PMC10804367 DOI: 10.1021/acschembio.3c00725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 12/10/2023] [Accepted: 12/12/2023] [Indexed: 12/28/2023]
Abstract
Machine learning (ML) models have made inroads into chemical sciences, with optimization of chemical reactions and prediction of biologically active molecules being prime examples thereof. These models excel where physical experiments are expensive or time-consuming, for example, due to large scales or the need for materials that are difficult to obtain. Studies of natural products suffer from these issues─this class of small molecules is known for its wealth of structural diversity and wide-ranging biological activities, but their investigation is hindered by poor synthetic accessibility and lack of scalability. To facilitate the evaluation of these molecules, we designed ML models that predict which natural products can interact with a particular target or a relevant pathway. Here, we focused on discovering natural products that are capable of modulating the 5-lipoxygenase (5-LO) pathway that plays key roles in lipid signaling and inflammation. These computational approaches led to the identification of nine natural products that either directly inhibit the activity of the 5-LO enzyme or affect the cellular 5-LO pathway. Further investigation of one of these molecules, deltonin, led us to discover a new cell-type-selective mechanism of action. Our ML approach helped deorphanize natural products as well as shed light on their mechanisms and can be broadly applied to other use cases in chemical biology.
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Affiliation(s)
- Sigitas Mikutis
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Stefanie Lawrinowitz
- Department
of Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, Friedrich Schiller University Jena, Philosophenweg 14, 07743 Jena, Germany
| | - Christian Kretzer
- Department
of Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, Friedrich Schiller University Jena, Philosophenweg 14, 07743 Jena, Germany
| | - Lavinia Dunsmore
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Laurynas Sketeris
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Tiago Rodrigues
- Instituto
de Investigação do Medicamento (iMed), Faculdade de
Farmácia, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
| | - Oliver Werz
- Department
of Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, Friedrich Schiller University Jena, Philosophenweg 14, 07743 Jena, Germany
| | - Gonçalo J. L. Bernardes
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
- Instituto
de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
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22
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Sarra H, Salim B, Hocine A. Modeling the Antiviral Activity of Ginkgo biloba Polyphenols against Variola: In Silico Exploration of Inhibitory Candidates for VarTMPK and HssTMPK Enzymes. Curr Drug Discov Technol 2024; 21:e101023221938. [PMID: 37861017 DOI: 10.2174/0115701638261541230922095853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 08/11/2023] [Accepted: 08/18/2023] [Indexed: 10/21/2023]
Abstract
BACKGROUND The aim of this study is to use modeling methods to estimate the antiviral activity of natural molecules extracted from Ginkgo biloba for the treatment of variola which is a zoonotic disease posing a growing threat to human survival. The recent spread of variola in nonendemic countries and the possibility of its use as a bioterrorism weapon have made it a global threat once again. Therefore, the search for new antiviral therapies with reduced side effects is necessary. METHODS In this study, we examined the interactions between polyphenolic compounds from Ginkgo biloba, a plant known for its antiviral activity, and two enzymes involved in variola treatment, VarTMPK and HssTMPK, using molecular docking. RESULTS The obtained docking scores showed that among the 152 selected polyphenolic compounds; many ligands had high inhibitory potential according to the energy affinity. By considering Lipinski's rules, we found that Liquiritin and Olivil molecules are the best candidates to be developed into drugs that inhibit VarTMPK because of their high obtained scores compared to reference ligands, and zero violations of Lipinski's rules. We also found that ginkgolic acids have good affinities with HssTMPK and acceptable physicochemical properties to be developed into drugs administered orally. CONCLUSION Based on the obtained scores and Lipinski's rules, Liquiritin, Olivil, and ginkgolic acids molecules showed interesting results for both studied enzymes, indicating the existence of promising and moderate activity of these polyphenols for the treatment of variola and for possible multi-targeting. Liquiritin has been shown to exhibit anti-inflammatory effects on various inflammation- related diseases such as skin injury, hepatic inflammatory injury, and rheumatoid arthritis. Olivil has been shown to have antioxidant activity. Olivil derivatives have also been studied for their potential use as anticancer agents. Ginkgolic acids have been shown to have antimicrobial and antifungal properties. However, ginkgolic acids are also known to cause allergic reactions in some people. Therefore, future studies should consider these results and explore the potential of these compounds as antiviral agents. Further experimental studies in-vitro and in-vivo are required to validate and scale up these findings.
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Affiliation(s)
- Hamdani Sarra
- Department of Chemistry, Faculty of Sciences, Abou Bekr Belkaïd University, Tlemcen 13000, P.O. Box 119, Algeria
- Laboratory of Natural and Bioactive Substances (LASNABIO), Department of Chemistry, Faculty of Sciences, Abou Bekr Belkaïd University, Tlemcen 13000, P.O. Box 119, Algeria
| | - Bouchentouf Salim
- Laboratory of Natural and Bioactive Substances (LASNABIO), Department of Chemistry, Faculty of Sciences, Abou Bekr Belkaïd University, Tlemcen 13000, P.O. Box 119, Algeria
- Department of Process Engineering, Faculty of Technology, Doctor Tahar Moulay University of Saida, Algeria, Saïda 20000, BP 138 cité EN-NASR, Algeria
| | - Allali Hocine
- Department of Chemistry, Faculty of Sciences, Abou Bekr Belkaïd University, Tlemcen 13000, P.O. Box 119, Algeria
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23
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Sukmarini L, Atikana A, Hertiani T. Antibiofilm activity of marine microbial natural products: potential peptide- and polyketide-derived molecules from marine microbes toward targeting biofilm-forming pathogens. J Nat Med 2024; 78:1-20. [PMID: 37930514 DOI: 10.1007/s11418-023-01754-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 10/05/2023] [Indexed: 11/07/2023]
Abstract
Controlling and treating biofilm-related infections is challenging because of the widespread presence of multidrug-resistant microbes. Biofilm, a naturally occurring matrix of microbial aggregates, has developed intricate and diverse resistance mechanisms against many currently used antibiotics. This poses a significant problem, especially for human health, including clinically chronic infectious diseases. Thus, there is an urgent need to search for and develop new and more effective antibiotics. As the marine environment is recognized as a promising reservoir of new biologically active molecules with potential pharmacological properties, marine natural products, particularly those of microbial origin, have emerged as a promising source of antibiofilm agents. Marine microbes represent an untapped source of secondary metabolites with antimicrobial activity. Furthermore, marine natural products, owing to their self-defense mechanisms and adaptation to harsh conditions, encompass a wide range of chemical compounds, including peptides and polyketides, which are primarily found in microbes. These molecules can be exploited to provide novel and unique structures for developing alternative antibiotics as effective antibiofilm agents. This review focuses on the possible antibiofilm mechanism of these marine microbial molecules against biofilm-forming pathogens. It provides an overview of biofilm development, its recalcitrant mode of action, strategies for the development of antibiofilm agents, and their assessments. The review also revisits some selected peptides and polyketides from marine microbes reported between 2016 and 2023, highlighting their moderate and considerable antibiofilm activities. Moreover, their antibiofilm mechanisms, such as adhesion modulation/inhibition targeting biofilm-forming pathogens, quorum sensing intervention and inhibition, and extracellular polymeric substance disruption, are highlighted herein.
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Affiliation(s)
- Linda Sukmarini
- Research Center for Applied Microbiology, National Research and Innovation Agency (BRIN), KST Soekarno, Jl. Raya Jakarta-Bogor Km. 46, Cibinong, West Java, 16911, Indonesia.
- Indonesian Biofilm Research Collaboration Center, Jl. Farmako Sekip Utara, Yogyakarta, 55281, Indonesia.
| | - Akhirta Atikana
- Research Center for Applied Microbiology, National Research and Innovation Agency (BRIN), KST Soekarno, Jl. Raya Jakarta-Bogor Km. 46, Cibinong, West Java, 16911, Indonesia
- Indonesian Biofilm Research Collaboration Center, Jl. Farmako Sekip Utara, Yogyakarta, 55281, Indonesia
| | - Triana Hertiani
- Indonesian Biofilm Research Collaboration Center, Jl. Farmako Sekip Utara, Yogyakarta, 55281, Indonesia.
- Pharmaceutical Biology Department, Faculty of Pharmacy, Gadjah Mada University, Jl. Sekip Utara, Yogyakarta, 55281, Indonesia.
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24
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Hui Z, Wen H, Zhu J, Deng H, Jiang X, Ye XY, Wang L, Xie T, Bai R. Discovery of plant-derived anti-tumor natural products: Potential leads for anti-tumor drug discovery. Bioorg Chem 2024; 142:106957. [PMID: 37939507 DOI: 10.1016/j.bioorg.2023.106957] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/14/2023] [Accepted: 10/31/2023] [Indexed: 11/10/2023]
Abstract
Natural products represent a paramount source of novel drugs. Numerous plant-derived natural products have demonstrated potent anti-tumor properties, thereby garnering considerable interest in their potential as anti-tumor drugs. This review compiles an overview of 242 recently discovered natural products, spanning the period from 2018 to the present. These natural products, which include 69 terpenoids, 42 alkaloids, 39 flavonoids, 21 steroids, 14 phenylpropanoids, 5 quinolines and 52 other compounds, are characterized by their respective chemical structures, anti-tumor activities, and mechanisms of action. By providing an essential reference and fresh insights, this review aims to support and inspire researchers engaged in the fields of natural products and anti-tumor drug discovery.
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Affiliation(s)
- Zi Hui
- School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, PR China; Key Laboratory of Elemene Class Anti-tumor Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, PR China
| | - Hao Wen
- School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, PR China; Key Laboratory of Elemene Class Anti-tumor Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, PR China
| | - Junlong Zhu
- School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, PR China; Key Laboratory of Elemene Class Anti-tumor Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, PR China
| | - Haowen Deng
- School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, PR China; Key Laboratory of Elemene Class Anti-tumor Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, PR China
| | - Xiaoying Jiang
- School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, PR China; Key Laboratory of Elemene Class Anti-tumor Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, PR China
| | - Xiang-Yang Ye
- School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, PR China; Key Laboratory of Elemene Class Anti-tumor Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, PR China
| | - Liwei Wang
- School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, PR China; Key Laboratory of Elemene Class Anti-tumor Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, PR China.
| | - Tian Xie
- School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, PR China; Key Laboratory of Elemene Class Anti-tumor Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, PR China.
| | - Renren Bai
- School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, PR China; Key Laboratory of Elemene Class Anti-tumor Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, PR China.
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25
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Affiliation(s)
- Sandip B Bharate
- Department of Natural Products & Medicinal Chemistry, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad-500007, India
| | - Craig W Lindsley
- Vanderbilt Institute of Chemical Biology Program in Drug Discovery, Department of Pharmacology, Vanderbilt Medical Center, Nashville, Tennessee 37240, United States
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26
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Quinn RJ, Mak T, Littler DR, Rossjohn J, Liu M. Discovery of Anti-SARS-CoV-2 Nsp9 Binders from Natural Products by a Native Mass Spectrometry Approach. JOURNAL OF NATURAL PRODUCTS 2023; 86:2630-2637. [PMID: 37993134 DOI: 10.1021/acs.jnatprod.3c00636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2023]
Abstract
The search for effective antiviral agents against SARS-CoV-2 remains a critical global endeavor. In this study, we focused on the viral nucleocapsid protein Nsp9, which is a key player in viral RNA replication and an attractive drug target. Employing a two-pronged approach, an in-house natural product library was screened using native mass spectrometry to identify compounds capable of binding to Nsp9. From the initial screening, apart from the previously reported hit oridonin (protein binding ratio of 0.56 in the initial screening, Kd = 7.2 ± 1.0 μM), we have identified a second Nsp9-interacting compound, the diterpenoid ryanodine, with a protein binding ratio of 0.3 and a Kd of 48.05 ± 5.03 μM. To gain deeper insights into the binding interactions and to explore potential structural requirements, the collision-induced affinity selection mass spectrometry (CIAS-MS) approach allowed us to identify six known oridonin analogues produced by the plant Rabdosia rubescens, each with varying affinities to Nsp9. Native MS validation of their individual binding activities to Nsp9 revealed that all analogues exhibited reduced affinity compared to oridonin. Structural-activity relationship analysis highlighted key functional groups, including 1-OH, 6-OH, 7-OH, and the enone moiety, which are crucial for Nsp9 binding. Combined data from our native mass spectrometry and CIAS-MS approaches provide valuable insights into the molecular interactions between Nsp9 and these compounds.
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Affiliation(s)
- Ronald J Quinn
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, QLD 4111, Australia
| | - Tin Mak
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, QLD 4111, Australia
| | - Dene R Littler
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800, Victoria, Australia
| | - Jamie Rossjohn
- Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800, Victoria, Australia
- Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, United Kingdom
| | - Miaomiao Liu
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, QLD 4111, Australia
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27
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Hassan AH, Bayoumi WA, El-Sayed SM, Phan TN, Oh T, Ham G, Mahmoud K, No JH, Lee YS. Design, Synthesis, and Repurposing of Rosmarinic Acid-β-Amino-α-Ketoamide Hybrids as Antileishmanial Agents. Pharmaceuticals (Basel) 2023; 16:1594. [PMID: 38004459 PMCID: PMC10675174 DOI: 10.3390/ph16111594] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 11/04/2023] [Accepted: 11/10/2023] [Indexed: 11/26/2023] Open
Abstract
A series of rosmarinic acid-β-amino-α-ketoamide hybrids were synthesized and rationally repurposed towards the identification of new antileishmanial hit compounds. Two hybrids, 2g and 2h, showed promising activity (IC50 values of 9.5 and 8.8 μM against Leishmania donovani promastigotes, respectively). Their activities were comparable to erufosine. In addition, cytotoxicity evaluation employing human THP-1 cells revealed that the two hybrids 2g and 2h possess no cytotoxic effects up to 100 µM, while erufosine possessed cytotoxicity with CC50 value of 19.4 µM. In silico docking provided insights into structure-activity relationship emphasizing the importance of the aliphatic chain at the α-carbon of the cinnamoyl carbonyl group establishing favorable binding interactions with LdCALP and LARG in both hybrids 2g and 2h. In light of these findings, hybrids 2g and 2h are suggested as potential safe antileishmanial hit compounds for further development of anti-leishmanial agents.
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Affiliation(s)
- Ahmed H.E. Hassan
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
- Medicinal Chemistry Laboratory, Department of Pharmacy, College of Pharmacy, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Waleed A. Bayoumi
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Selwan M. El-Sayed
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Trong-Nhat Phan
- Institute of Applied Science and Technology, School of Technology, Van Lang University, Ho Chi Minh City 700000, Vietnam
- Faculty of Applied Technology, School of Technology, Van Lang University, Ho Chi Minh City 700000, Vietnam
| | - Taegeun Oh
- Department of Fundamental Pharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Gyeongpyo Ham
- Department of Fundamental Pharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Kazem Mahmoud
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Egyptian Russian University, Badr City 11829, Egypt
| | - Joo Hwan No
- Host-Parasite Research Laboratory, Institut Pasteur Korea, Seongnam-si 13488, Gyeonggi-do, Republic of Korea
| | - Yong Sup Lee
- Medicinal Chemistry Laboratory, Department of Pharmacy, College of Pharmacy, Kyung Hee University, Seoul 02447, Republic of Korea
- Department of Fundamental Pharmaceutical Sciences, Kyung Hee University, Seoul 02447, Republic of Korea
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28
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Wohlgemuth R. Synthesis of Metabolites and Metabolite-like Compounds Using Biocatalytic Systems. Metabolites 2023; 13:1097. [PMID: 37887422 PMCID: PMC10608848 DOI: 10.3390/metabo13101097] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 10/13/2023] [Accepted: 10/15/2023] [Indexed: 10/28/2023] Open
Abstract
Methodologies for the synthesis and purification of metabolites, which have been developed following their discovery, analysis, and structural identification, have been involved in numerous life science milestones. The renewed focus on the small molecule domain of biological cells has also created an increasing awareness of the rising gap between the metabolites identified and the metabolites which have been prepared as pure compounds. The design and engineering of resource-efficient and straightforward synthetic methodologies for the production of the diverse and numerous metabolites and metabolite-like compounds have attracted much interest. The variety of metabolic pathways in biological cells provides a wonderful blueprint for designing simplified and resource-efficient synthetic routes to desired metabolites. Therefore, biocatalytic systems have become key enabling tools for the synthesis of an increasing number of metabolites, which can then be utilized as standards, enzyme substrates, inhibitors, or other products, or for the discovery of novel biological functions.
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Affiliation(s)
- Roland Wohlgemuth
- MITR, Institute of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego Street 116, 90-924 Lodz, Poland;
- Swiss Coordination Committee Biotechnology (SKB), 8021 Zurich, Switzerland
- European Society of Applied Biocatalysis (ESAB), 1000 Brussels, Belgium
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29
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Casamajo A, Yu Y, Schnepel C, Morrill C, Barker R, Levy CW, Finnigan J, Spelling V, Westerlund K, Petchey M, Sheppard RJ, Lewis RJ, Falcioni F, Hayes MA, Turner NJ. Biocatalysis in Drug Design: Engineered Reductive Aminases (RedAms) Are Used to Access Chiral Building Blocks with Multiple Stereocenters. J Am Chem Soc 2023; 145:22041-22046. [PMID: 37782882 PMCID: PMC10571080 DOI: 10.1021/jacs.3c07010] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Indexed: 10/04/2023]
Abstract
Novel building blocks are in constant demand during the search for innovative bioactive small molecule therapeutics by enabling the construction of structure-activity-property-toxicology relationships. Complex chiral molecules containing multiple stereocenters are an important component in compound library expansion but can be difficult to access by traditional organic synthesis. Herein, we report a biocatalytic process to access a specific diastereomer of a chiral amine building block used in drug discovery. A reductive aminase (RedAm) was engineered following a structure-guided mutagenesis strategy to produce the desired isomer. The engineered RedAm (IR-09 W204R) was able to generate the (S,S,S)-isomer 3 in 45% conversion and 95% ee from the racemic ketone 2. Subsequent palladium-catalyzed deallylation of 3 yielded the target primary amine 4 in a 73% yield. This engineered biocatalyst was used at preparative scale and represents a potential starting point for further engineering and process development.
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Affiliation(s)
- Arnau
Rué Casamajo
- Department
of Chemistry, University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, United
Kingdom
| | - Yuqi Yu
- Department
of Chemistry, University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, United
Kingdom
| | - Christian Schnepel
- School
of Engineering Sciences in Chemistry, Biotechnology and Health, Department
of Industrial Biotechnology, KTH Royal Institute of Technology, AlbaNova University Center, 11421 Stockholm, Sweden
| | - Charlotte Morrill
- Department
of Chemistry, University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, United
Kingdom
| | - Rhys Barker
- Department
of Chemistry, University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, United
Kingdom
| | - Colin W. Levy
- Department
of Chemistry, University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, United
Kingdom
| | - James Finnigan
- Prozomix
Ltd, Building 4, West
End Ind. Estate, Haltwhistle NE49 9HA, United Kingdom
| | - Victor Spelling
- Early
Chemical Development, Pharmaceutical Sciences, Biopharmaceuticals
R&D, AstraZeneca, Mölndal, 431 50 Gothenburg, Sweden
| | - Kristina Westerlund
- Medicinal
Chemistry, Research and Early Development; Cardiovascular, Renal and
Metabolism, Biopharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, Mölndal, 431 50 Gothenburg Sweden
| | - Mark Petchey
- Compound
Synthesis and Management, Discovery Sciences, Biopharmaceuticals R&D, AstraZeneca, Mölndal, 431 50 Gothenburg, Sweden
| | - Robert J. Sheppard
- Medicinal
Chemistry, Research and Early Development; Cardiovascular, Renal and
Metabolism, Biopharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, Mölndal, 431 50 Gothenburg Sweden
| | - Richard J. Lewis
- Department
of Medicinal Chemistry, Research and Early Development, Respiratory
and Immunology (R&I), BioPharmaceuticals R&D, AstraZeneca, 43183 Mölndal, Sweden
| | - Francesco Falcioni
- Early
Chemical Development, Pharmaceutical Sciences, Biopharmaceuticals
R&D, AstraZeneca, CB21 6GP Cambridge, United Kingdom
| | - Martin A. Hayes
- Compound
Synthesis and Management, Discovery Sciences, Biopharmaceuticals R&D, AstraZeneca, Mölndal, 431 50 Gothenburg, Sweden
| | - Nicholas J. Turner
- Department
of Chemistry, University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, United
Kingdom
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30
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Finnigan W, Lubberink M, Hepworth LJ, Citoler J, Mattey AP, Ford GJ, Sangster J, Cosgrove SC, da Costa BZ, Heath RS, Thorpe TW, Yu Y, Flitsch SL, Turner NJ. RetroBioCat Database: A Platform for Collaborative Curation and Automated Meta-Analysis of Biocatalysis Data. ACS Catal 2023; 13:11771-11780. [PMID: 37671181 PMCID: PMC10476152 DOI: 10.1021/acscatal.3c01418] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 06/26/2023] [Indexed: 09/07/2023]
Abstract
Despite the increasing use of biocatalysis for organic synthesis, there are currently no databases that adequately capture synthetic biotransformations. The lack of a biocatalysis database prevents accelerating biocatalyst characterization efforts from being leveraged to quickly identify candidate enzymes for reactions or cascades, slowing their development. The RetroBioCat Database (available at retrobiocat.com) addresses this gap by capturing information on synthetic biotransformations and providing an analysis platform that allows biocatalysis data to be searched and explored through a range of highly interactive data visualization tools. This database makes it simple to explore available enzymes, their substrate scopes, and how characterized enzymes are related to each other and the wider sequence space. Data entry is facilitated through an openly accessible curation platform, featuring automated tools to accelerate the process. The RetroBioCat Database democratizes biocatalysis knowledge and has the potential to accelerate biocatalytic reaction development, making it a valuable resource for the community.
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Affiliation(s)
- William Finnigan
- Department of Chemistry, Manchester Institute of Biotechnology, University
of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | | | - Lorna J. Hepworth
- Department of Chemistry, Manchester Institute of Biotechnology, University
of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Joan Citoler
- Department of Chemistry, Manchester Institute of Biotechnology, University
of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Ashley P. Mattey
- Department of Chemistry, Manchester Institute of Biotechnology, University
of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Grayson J. Ford
- Department of Chemistry, Manchester Institute of Biotechnology, University
of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Jack Sangster
- Department of Chemistry, Manchester Institute of Biotechnology, University
of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | | | - Bruna Zucoloto da Costa
- Department of Chemistry, Manchester Institute of Biotechnology, University
of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Rachel S. Heath
- Department of Chemistry, Manchester Institute of Biotechnology, University
of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | | | - Yuqi Yu
- Department of Chemistry, Manchester Institute of Biotechnology, University
of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Sabine L. Flitsch
- Department of Chemistry, Manchester Institute of Biotechnology, University
of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Nicholas J. Turner
- Department of Chemistry, Manchester Institute of Biotechnology, University
of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
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31
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Young RJ. Today's drug discovery and the shadow of the rule of 5. Expert Opin Drug Discov 2023; 18:965-972. [PMID: 37378429 DOI: 10.1080/17460441.2023.2228199] [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: 04/12/2023] [Accepted: 06/19/2023] [Indexed: 06/29/2023]
Abstract
INTRODUCTION The rule of 5 developed by Lipinski et al., a landmark and prescient piece of scholarship, focused the minds of drug hunters by systematically characterizing the physical make-up of drug molecules for the first time, noting many sub-optimal compounds identified by high-throughput screening practices. Its profound influence on thinking and practices, whilst providing benefit, perhaps etched the guidelines too strongly in the minds of some drug hunters who applied the bounds too literally without understanding the implications of the underlying statistics. AREAS COVERED This opinion is based on recent key developments that take thinking, measurements, and standards beyond those first set out, particularly the influences of molecular weight and the understanding, measurement, and calculation of lipophilicity. EXPERT OPINION Techniques and technologies for physicochemical estimations set new standards. It is timely to celebrate the significance and influence of the rule of 5, whilst taking thinking to new levels with better characterizations. The shadow of the rule of 5 may be long, but it is not dark, as new measurements, predictions and principles emerge as guiding lights in the design and prioritization of higher-quality molecules redefining the meaning of beyond the rule of 5.
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Affiliation(s)
- Robert J Young
- Blue Burgundy (Drug Discovery Consultancy) Ltd, Bedford, UK
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32
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Jacobson KA, Pradhan B, Wen Z, Pramanik A. New paradigms in purinergic receptor ligand discovery. Neuropharmacology 2023; 230:109503. [PMID: 36921890 PMCID: PMC10233512 DOI: 10.1016/j.neuropharm.2023.109503] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 02/28/2023] [Accepted: 03/11/2023] [Indexed: 03/14/2023]
Abstract
The discovery and clinical implementation of modulators of adenosine, P2Y and P2X receptors (comprising nineteen subtypes) have progressed dramatically in ∼50 years since Burnstock's definition of purinergic signaling. Although most clinical trials of selective ligands (agonists and antagonists) of certain purinergic receptors failed, there is a renewed impetus to redirect efforts to new disease conditions and the discovery of more selective or targeted compounds with potentially reduced side effects, such as biased GPCR agonists. The elucidation of new receptor and enzyme structures is steering rational design of potent and selective agonists, antagonists, allosteric modulators and inhibitors. A2A adenosine receptor (AR) antagonists are being applied to neurodegenerative conditions and cancer immunotherapy. A3AR agonists have potential for treating chronic inflammation (e.g. psoriasis), stroke and pain, as well as cancer. P2YR modulators are being considered for treating inflammation, metabolic disorders, acute kidney injury, cancer, pain and other conditions, often with an immune mechanism. ADP-activated P2Y12R antagonists are widely used as antithrombotic drugs, while their repurposing toward neuroinflammation is considered. P2X3 antagonists have been in clinical trials for chronic cough. P2X7 antagonists have been in clinical trials for inflammatory diseases and depression (compounds that penetrate the blood-brain barrier). Thus, purinergic signaling is now recognized as an immense regulatory system in the body for rebalancing tissues and organs under stress, which can be adjusted by drug intervention for therapeutic purposes. The lack of success of many previous clinical trials can be overcome given more advanced pharmacokinetic and pharmacodynamic approaches, including structure-based drug design, prodrugs and biased signaling. This article is part of the Special Issue on "Purinergic Signaling: 50 years".
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Affiliation(s)
- Kenneth A Jacobson
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD, 20892, USA.
| | - Balaram Pradhan
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD, 20892, USA.
| | - Zhiwei Wen
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD, 20892, USA.
| | - Asmita Pramanik
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD, 20892, USA.
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33
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Debon A, Siirola E, Snajdrova R. Enzymatic Bioconjugation: A Perspective from the Pharmaceutical Industry. JACS AU 2023; 3:1267-1283. [PMID: 37234110 PMCID: PMC10207132 DOI: 10.1021/jacsau.2c00617] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 01/10/2023] [Accepted: 01/10/2023] [Indexed: 05/27/2023]
Abstract
Enzymes have firmly established themselves as bespoke catalysts for small molecule transformations in the pharmaceutical industry, from early research and development stages to large-scale production. In principle, their exquisite selectivity and rate acceleration can also be leveraged for modifying macromolecules to form bioconjugates. However, available catalysts face stiff competition from other bioorthogonal chemistries. In this Perspective, we seek to illuminate applications of enzymatic bioconjugation in the face of an expanding palette of new drug modalities. With these applications, we wish to highlight some examples of current successes and pitfalls of using enzymes for bioconjugation along the pipeline and try to illustrate opportunities for further development.
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Affiliation(s)
- Aaron Debon
- Global
Discovery Chemistry, Novartis Institute
for Biomedical Research, Basel 4108, Switzerland
| | - Elina Siirola
- Global
Discovery Chemistry, Novartis Institute
for Biomedical Research, Basel 4108, Switzerland
| | - Radka Snajdrova
- Global
Discovery Chemistry, Novartis Institute
for Biomedical Research, Basel 4108, Switzerland
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34
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Chiodi D, Ishihara Y. "Magic Chloro": Profound Effects of the Chlorine Atom in Drug Discovery. J Med Chem 2023; 66:5305-5331. [PMID: 37014977 DOI: 10.1021/acs.jmedchem.2c02015] [Citation(s) in RCA: 60] [Impact Index Per Article: 60.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2023]
Abstract
Chlorine is one of the most common atoms present in small-molecule drugs beyond carbon, hydrogen, nitrogen, and oxygen. There are currently more than 250 FDA-approved chlorine-containing drugs, yet the beneficial effect of the chloro substituent has not yet been reviewed. The seemingly simple substitution of a hydrogen atom (R = H) with a chlorine atom (R = Cl) can result in remarkable improvements in potency of up to 100,000-fold and can lead to profound effects on pharmacokinetic parameters including clearance, half-life, and drug exposure in vivo. Following the literature terminology of the "magic methyl effect" in drugs, the term "magic chloro effect" has been coined herein. Although reports of 500-fold or 1000-fold potency improvements are often serendipitous discoveries that can be considered "magical" rather than planned, hypotheses made to explain the magic chloro effect can lead to lessons that accelerate the cycle of drug discovery.
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Affiliation(s)
- Debora Chiodi
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Yoshihiro Ishihara
- Department of Chemistry, Vividion Therapeutics, 5820 Nancy Ridge Drive, San Diego, California 92121, United States
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35
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France SP, Lewis RD, Martinez CA. The Evolving Nature of Biocatalysis in Pharmaceutical Research and Development. JACS AU 2023; 3:715-735. [PMID: 37006753 PMCID: PMC10052283 DOI: 10.1021/jacsau.2c00712] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/13/2023] [Accepted: 02/13/2023] [Indexed: 06/19/2023]
Abstract
Biocatalysis is a highly valued enabling technology for pharmaceutical research and development as it can unlock synthetic routes to complex chiral motifs with unparalleled selectivity and efficiency. This perspective aims to review recent advances in the pharmaceutical implementation of biocatalysis across early and late-stage development with a focus on the implementation of processes for preparative-scale syntheses.
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36
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Tangara S, Faïon L, Piveteau C, Capet F, Godelier R, Michel M, Flipo M, Deprez B, Willand N, Villemagne B. Rapid and Efficient Access to Novel Bio-Inspired 3-Dimensional Tricyclic SpiroLactams as Privileged Structures via Meyers’ Lactamization. Pharmaceuticals (Basel) 2023; 16:ph16030413. [PMID: 36986512 PMCID: PMC10054226 DOI: 10.3390/ph16030413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 03/02/2023] [Indexed: 03/11/2023] Open
Abstract
The concept of privileged structure has been used as a fruitful approach for the discovery of novel biologically active molecules. A privileged structure is defined as a semi-rigid scaffold able to display substituents in multiple spatial directions and capable of providing potent and selective ligands for different biological targets through the modification of those substituents. On average, these backbones tend to exhibit improved drug-like properties and therefore represent attractive starting points for hit-to-lead optimization programs. This article promotes the rapid, reliable, and efficient synthesis of novel, highly 3-dimensional, and easily functionalized bio-inspired tricyclic spirolactams, as well as an analysis of their drug-like properties.
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Affiliation(s)
- Salia Tangara
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177—Drugs and Molecules for Living Systems, F-59000 Lille, France
| | - Léo Faïon
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177—Drugs and Molecules for Living Systems, F-59000 Lille, France
| | - Catherine Piveteau
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177—Drugs and Molecules for Living Systems, F-59000 Lille, France
| | - Frédéric Capet
- Univ. Lille, CNRS, Centrale Lille, ENSCL, Univ. Artois, UMR 8181—UCCS—Unité de Catalyse et Chimie du Solide, F-59000 Lille, France
| | - Romain Godelier
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177—Drugs and Molecules for Living Systems, F-59000 Lille, France
| | - Marion Michel
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177—Drugs and Molecules for Living Systems, F-59000 Lille, France
| | - Marion Flipo
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177—Drugs and Molecules for Living Systems, F-59000 Lille, France
| | - Benoit Deprez
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177—Drugs and Molecules for Living Systems, F-59000 Lille, France
| | - Nicolas Willand
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177—Drugs and Molecules for Living Systems, F-59000 Lille, France
| | - Baptiste Villemagne
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177—Drugs and Molecules for Living Systems, F-59000 Lille, France
- Correspondence:
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Dekker T, Harteveld JW, Wágner G, de Vries MCM, Custers H, van de Stolpe AC, de Esch IJP, Wijtmans M. Green Drug Discovery: Novel Fragment Space from the Biomass-Derived Molecule Dihydrolevoglucosenone (Cyrene TM). Molecules 2023; 28:molecules28041777. [PMID: 36838763 PMCID: PMC9967789 DOI: 10.3390/molecules28041777] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/23/2023] [Accepted: 01/25/2023] [Indexed: 02/16/2023] Open
Abstract
Biomass-derived molecules can provide a basis for sustainable drug discovery. However, their full exploration is hampered by the dominance of millions of old-fashioned screening compounds in classical high-throughput screening (HTS) libraries frequently utilized. We propose a fragment-based drug discovery (FBDD) approach as an efficient method to navigate biomass-derived drug space. Here, we perform a proof-of-concept study with dihydrolevoglucosenone (CyreneTM), a pyrolysis product of cellulose. Diverse synthetic routes afforded a 100-membered fragment library with a diversity in functional groups appended. The library overall performs well in terms of novelty, physicochemical properties, aqueous solubility, stability, and three-dimensionality. Our study suggests that Cyrene-based fragments are a valuable green addition to the drug discovery toolbox. Our findings can help in paving the way for new hit drug candidates that are based on renewable resources.
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Revillo Imbernon J, Chiesa L, Kellenberger E. Mining the Protein Data Bank to inspire fragment library design. Front Chem 2023; 11:1089714. [PMID: 36846858 PMCID: PMC9950109 DOI: 10.3389/fchem.2023.1089714] [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: 11/04/2022] [Accepted: 01/27/2023] [Indexed: 02/12/2023] Open
Abstract
The fragment approach has emerged as a method of choice for drug design, as it allows difficult therapeutic targets to be addressed. Success lies in the choice of the screened chemical library and the biophysical screening method, and also in the quality of the selected fragment and structural information used to develop a drug-like ligand. It has recently been proposed that promiscuous compounds, i.e., those that bind to several proteins, present an advantage for the fragment approach because they are likely to give frequent hits in screening. In this study, we searched the Protein Data Bank for fragments with multiple binding modes and targeting different sites. We identified 203 fragments represented by 90 scaffolds, some of which are not or hardly present in commercial fragment libraries. By contrast to other available fragment libraries, the studied set is enriched in fragments with a marked three-dimensional character (download at 10.5281/zenodo.7554649).
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Affiliation(s)
- Julia Revillo Imbernon
- Laboratoire d’Innovation Thérapeutique, Faculté de Pharmacie, UMR7200 CNRS Université de Strasbourg, Illkirch-Graffenstaden, France
| | - Luca Chiesa
- Laboratoire d’Innovation Thérapeutique, Faculté de Pharmacie, UMR7200 CNRS Université de Strasbourg, Illkirch-Graffenstaden, France
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