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Yang T, Cao T, Yang X, Wang G, Li Y. Elucidation of the key therapeutic targets and potential mechanisms of Andrographolide multi-targets against osteoarthritis via network pharmacological analysis and experimental validation. Gene 2024; 911:148351. [PMID: 38462021 DOI: 10.1016/j.gene.2024.148351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 02/26/2024] [Accepted: 03/07/2024] [Indexed: 03/12/2024]
Abstract
OBJECTIVE Our purpose is to unveil Andrographolide's potential multi-target and multi-mechanism therapeutic effects in treating OA via systematic network pharmacological analysis and cell experimental validation. MATERIALS AND METHODS Initially, we gathered data from Andrographolide and OA-related databases to obtain information on Andrographolide's biological properties and the targets linked with OA. We developed a bioinformatic network about Andrographolide and OA, whereby we analyzed the network to identify potential therapeutic targets and mechanisms of action of Andrographolide. Subsequently, we used molecular docking to analyze the binding sites of Andrographolide to the target proteins. At the same time, SDF-1 was used to construct an OA cell model to verify the therapeutic effect of Andrographolide on OA and its effect on target proteins. RESULTS Our experimental results show that Andrographolide has excellent pharmaceutical properties, by Lipinski's rules for drugs, suggesting that this compound can be considered to have a high therapeutic potential in drug development. 233 targets were preliminarily investigated, the mechanisms through which Andrographolide targets OA primarily involve the TNF signaling pathway, PI3K-AKT signaling pathway, IL-17 signaling pathway, and TLR signaling pathway. These mechanisms target OA by influencing immune and inflammatory responses in the joints, regulating apoptosis to prevent chondrocyte death. Finally, TNF-α, STAT3, TP53, IL-6, JUN, IL-1β, HIF-1α, TGF-β1, and AKT1 were identified as 9 key targets of Andrographolide anti-OA. In addition, our molecular docking analyzes with cell experimental validation further confirm the network pharmacology results. According to our molecular docking results, Andrographolide can bind to all the hub target proteins and has a good binding ability (binding energy < -5 kcal/mol), with the strongest binding affinity to AKT1 of -9.2 kcal/ mol. The results of cell experiments showed that Andrographolide treatment significantly increased the cell viability and the expression of COL2A1 and ACAN proteins. Moreover, 30 μM Andrographolide significantly reversed SDF-1-induced increases in the protein expression of TNF-α, STAT3, TP53, IL-6, JUN, IL-1β, HIF-1α, and TGF-β1, and decreases in the protein expression of AKT1. CONCLUSION This study provides a comprehensive understanding of the potential therapeutic targets and mechanisms of action of Andrographolide in OA treatment. Our findings suggest that Andrographolide is a promising candidate for drug development in the management of OA.
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Affiliation(s)
- Tengyun Yang
- Department of Sports Medicine, The First Affiliated Hospital, Kunming Medical University, Kunming, 650032, Yunnan, China
| | - Tingting Cao
- School of Pharmaceutical Science and Yunnan Key Laboratory of Pharmacology of Natural Products, Kunming Medical University, Kunming, 650500, Yunnan, China
| | - Xianguang Yang
- Department of Sports Medicine, The First Affiliated Hospital, Kunming Medical University, Kunming, 650032, Yunnan, China
| | - Guoliang Wang
- Department of Sports Medicine, The First Affiliated Hospital, Kunming Medical University, Kunming, 650032, Yunnan, China
| | - Yanlin Li
- Department of Sports Medicine, The First Affiliated Hospital, Kunming Medical University, Kunming, 650032, Yunnan, China.
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2
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Dudley JA, Park S, Cho O, Wells NGM, MacDonald ME, Blejec KM, Fetene E, Zanderigo E, Houliston S, Liddle JC, Dashnaw CM, Sabo TM, Shaw BF, Balsbaugh JL, Rocklin GJ, Smith CA. Heat-induced structural and chemical changes to a computationally designed miniprotein. Protein Sci 2024; 33:e4991. [PMID: 38757381 PMCID: PMC11099715 DOI: 10.1002/pro.4991] [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: 12/11/2023] [Revised: 03/22/2024] [Accepted: 03/28/2024] [Indexed: 05/18/2024]
Abstract
The de novo design of miniprotein inhibitors has recently emerged as a new technology to create proteins that bind with high affinity to specific therapeutic targets. Their size, ease of expression, and apparent high stability makes them excellent candidates for a new class of protein drugs. However, beyond circular dichroism melts and hydrogen/deuterium exchange experiments, little is known about their dynamics, especially at the elevated temperatures they seemingly tolerate quite well. To address that and gain insight for future designs, we have focused on identifying unintended and previously overlooked heat-induced structural and chemical changes in a particularly stable model miniprotein, EHEE_rd2_0005. Nuclear magnetic resonance (NMR) studies suggest the presence of dynamics on multiple time and temperature scales. Transiently elevating the temperature results in spontaneous chemical deamidation visible in the NMR spectra, which we validate using both capillary electrophoresis and mass spectrometry (MS) experiments. High temperatures also result in greatly accelerated intrinsic rates of hydrogen exchange and signal loss in NMR heteronuclear single quantum coherence spectra from local unfolding. These losses are in excellent agreement with both room temperature hydrogen exchange experiments and hydrogen bond disruption in replica exchange molecular dynamics simulations. Our analysis reveals important principles for future miniprotein designs and the potential for high stability to result in long-lived alternate conformational states.
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Affiliation(s)
- Joshua A. Dudley
- Department of ChemistryWesleyan UniversityMiddletownConnecticutUSA
| | - Sojeong Park
- Department of ChemistryWesleyan UniversityMiddletownConnecticutUSA
| | - Oliver Cho
- Department of ChemistryWesleyan UniversityMiddletownConnecticutUSA
| | | | | | | | - Emmanuel Fetene
- Department of ChemistryWesleyan UniversityMiddletownConnecticutUSA
| | - Eric Zanderigo
- Department of ChemistryWesleyan UniversityMiddletownConnecticutUSA
| | - Scott Houliston
- Structural Genomics ConsortiumUniversity of TorontoTorontoOntarioCanada
| | - Jennifer C. Liddle
- Proteomics and Metabolomics FacilityUniversity of ConnecticutStorrsConnecticutUSA
| | - Chad M. Dashnaw
- Department of Chemistry and BiochemistryBaylor UniversityWacoTexasUSA
| | - T. Michael Sabo
- Department of Medicine and Brown Cancer CenterUniversity of LouisvilleLouisvilleKentuckyUSA
| | - Bryan F. Shaw
- Department of Chemistry and BiochemistryBaylor UniversityWacoTexasUSA
| | - Jeremy L. Balsbaugh
- Proteomics and Metabolomics FacilityUniversity of ConnecticutStorrsConnecticutUSA
| | - Gabriel J. Rocklin
- Department of Pharmacology and Center for Synthetic BiologyNorthwestern UniversityEvanstonIllinoisUSA
| | - Colin A. Smith
- Department of ChemistryWesleyan UniversityMiddletownConnecticutUSA
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3
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Occhipinti G, Laudani C, Spagnolo M, Finocchiaro S, Mazzone PM, Faro DC, Mauro MS, Rochira C, Agnello F, Giacoppo D, Ammirabile N, Landolina D, Imbesi A, Sangiorgio G, Greco A, Capodanno D. Pharmacological and clinical appraisal of factor XI inhibitor drugs. EUROPEAN HEART JOURNAL. CARDIOVASCULAR PHARMACOTHERAPY 2024; 10:245-258. [PMID: 38196141 DOI: 10.1093/ehjcvp/pvae002] [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: 11/02/2023] [Revised: 12/04/2023] [Accepted: 01/08/2024] [Indexed: 01/11/2024]
Abstract
The evolution of anticoagulation therapy, from vitamin K antagonists to the advent of direct oral anticoagulants (DOACs) almost two decades ago, marks significant progress. Despite improved safety demonstrated in pivotal trials and post-marketing observations, persistent concerns exist, particularly regarding bleeding risk and the absence of therapeutic indications in specific subgroups or clinical contexts. Factor XI (FXI) has recently emerged as a pivotal contributor to intraluminal thrombus formation and growth, playing a limited role in sealing vessel wall injuries. Inhibiting FXI presents an opportunity to decouple thrombosis from haemostasis, addressing concerns related to bleeding events while safeguarding against thromboembolic events. Notably, FXI inhibition holds promise for patients with end-stage renal disease or cancer, where clear indications for DOACs are currently lacking. Various compounds have undergone design, testing, and progression to phase 2 clinical trials, demonstrating a generally favourable safety and tolerability profile. However, validation through large-scale phase 3 trials with sufficient power to assess both safety and efficacy outcomes is needed. This review comprehensively examines FXI inhibitors, delving into individual classes, exploring their pharmacological properties, evaluating the latest evidence from randomized trials, and offering insights into future perspectives.
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Affiliation(s)
- Giovanni Occhipinti
- Division of Cardiology, Azienda Ospedaliero-Universitaria Policlinico "G. Rodolico-San Marco", University of Catania, Catania 95123, Italy
| | - Claudio Laudani
- Division of Cardiology, Azienda Ospedaliero-Universitaria Policlinico "G. Rodolico-San Marco", University of Catania, Catania 95123, Italy
| | - Marco Spagnolo
- Division of Cardiology, Azienda Ospedaliero-Universitaria Policlinico "G. Rodolico-San Marco", University of Catania, Catania 95123, Italy
| | - Simone Finocchiaro
- Division of Cardiology, Azienda Ospedaliero-Universitaria Policlinico "G. Rodolico-San Marco", University of Catania, Catania 95123, Italy
| | - Placido Maria Mazzone
- Division of Cardiology, Azienda Ospedaliero-Universitaria Policlinico "G. Rodolico-San Marco", University of Catania, Catania 95123, Italy
| | - Denise Cristiana Faro
- Division of Cardiology, Azienda Ospedaliero-Universitaria Policlinico "G. Rodolico-San Marco", University of Catania, Catania 95123, Italy
| | - Maria Sara Mauro
- Division of Cardiology, Azienda Ospedaliero-Universitaria Policlinico "G. Rodolico-San Marco", University of Catania, Catania 95123, Italy
| | - Carla Rochira
- Division of Cardiology, Azienda Ospedaliero-Universitaria Policlinico "G. Rodolico-San Marco", University of Catania, Catania 95123, Italy
| | - Federica Agnello
- Division of Cardiology, Azienda Ospedaliero-Universitaria Policlinico "G. Rodolico-San Marco", University of Catania, Catania 95123, Italy
| | - Daniele Giacoppo
- Division of Cardiology, Azienda Ospedaliero-Universitaria Policlinico "G. Rodolico-San Marco", University of Catania, Catania 95123, Italy
| | - Nicola Ammirabile
- Division of Cardiology, Azienda Ospedaliero-Universitaria Policlinico "G. Rodolico-San Marco", University of Catania, Catania 95123, Italy
| | - Davide Landolina
- Division of Cardiology, Azienda Ospedaliero-Universitaria Policlinico "G. Rodolico-San Marco", University of Catania, Catania 95123, Italy
| | - Antonino Imbesi
- Division of Cardiology, Azienda Ospedaliero-Universitaria Policlinico "G. Rodolico-San Marco", University of Catania, Catania 95123, Italy
| | - Giuseppe Sangiorgio
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania 95123, Italy
| | - Antonio Greco
- Division of Cardiology, Azienda Ospedaliero-Universitaria Policlinico "G. Rodolico-San Marco", University of Catania, Catania 95123, Italy
| | - Davide Capodanno
- Division of Cardiology, Azienda Ospedaliero-Universitaria Policlinico "G. Rodolico-San Marco", University of Catania, Catania 95123, Italy
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4
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Alharbi B, Alharethi SH, Al-Soud WA, Ahmed Al-Keridis L, Aljohani AA, Jairajpuri DS, Alshammari N, Adnan M. Exploring the potential of phytochemicals as inhibitors of 3'-phosphoadenosine 5'-phosphosulfate synthase 1 targeting cancer therapy. J Biomol Struct Dyn 2024; 42:3193-3203. [PMID: 37184152 DOI: 10.1080/07391102.2023.2212810] [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: 02/09/2023] [Accepted: 05/03/2023] [Indexed: 05/16/2023]
Abstract
3'-phosphoadenosine 5'-phosphosulfate synthase 1 (PAPSS1) is an enzyme that critically synthesises the biologically active form of sulfate (PAPS) for all sulfation reactions. The discovery of PAPSS1 as a possible drug target for cancer therapy, specifically in non-small cell lung cancer, has prompted us to investigate potential small-molecule inhibitors of PAPSS1. Here, a structure-based virtual screening method was used to search for phytochemicals in the IMPPAT database to find potential inhibitors of PAPSS1. The primary hits were selected based on their physicochemical, ADMET, and drug-like properties. Then, the binding affinities were calculated and analyzed the interactions to identify safer and more effective hits. The research identified two phytochemicals, Guggulsterone and Corylin, that exhibited significant affinity and specific interaction with the ATP-binding pocket of PAPSS1. Structural observations made by molecular docking were further accompanied by molecular dynamics (MD) simulations and principal component analysis (PCA) to examine the conformational changes and stability of PAPSS1 with the elucidated compounds Guggulsterone and Corylin. MD simulation results suggested that the binding of Guggulsterone and Corylin stabilizes the PAPSS1 structure, leading to fewer conformational changes. This implies that these compounds may be useful in developing PAPSS1 inhibitors for the therapeutic development against non-small cell lung cancer (NSCLC). This study highlights the potential of phytochemicals as PAPSS1 inhibitors and the utility of computational approaches in drug discovery.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Bandar Alharbi
- Department of Medical Laboratory Science, College of Applied Medical Sciences, University of Ha'il, Ha'il, Saudi Arabia
| | - Salem Hussain Alharethi
- Department of Biological Science, College of Arts and Science, Najran University, Najran, Saudi Arabia
| | - Waleed Abu Al-Soud
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Jouf University, Sakaka, Saudi Arabia
| | - Lamya Ahmed Al-Keridis
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Abdullah A Aljohani
- Department of Clinical laboratory Science, College of Applied Medical Sciences-Qurayyat, Jouf University, Sakaka, Saudi Arabia
| | - Deeba Shamim Jairajpuri
- Department of Medical Biochemistry, College of Medicine and Medical Sciences, Arabian Gulf University, Manama, Bahrain
| | - Nawaf Alshammari
- Department of Biology, College of Science, University of Ha'il, Ha'il, Saudi Arabia
| | - Mohd Adnan
- Department of Biology, College of Science, University of Ha'il, Ha'il, Saudi Arabia
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5
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Selvaraj C, Pedone E, Lee JK, Singh SK. Editorial: Molecular level atomistic and structural insights on biological macromolecules, inhibition, and dynamics studies. Front Mol Biosci 2024; 11:1362215. [PMID: 38516195 PMCID: PMC10955358 DOI: 10.3389/fmolb.2024.1362215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 02/19/2024] [Indexed: 03/23/2024] Open
Affiliation(s)
- Chandrabose Selvaraj
- Computational and Structural Research in Drug Discovery Lab (CSRDD), Center for Global Health Research, Saveetha Medical College, Saveetha Institute of Medical and Technical Sciences, Chennai, Tamil Nadu, India
| | - Emilia Pedone
- Institute of Biostructures and Bioimaging, CNR, Naples, Italy
| | - Jung-Kul Lee
- Department of Chemical Engineering, Konkuk University, Seoul, Republic of Korea
| | - Sanjeev Kumar Singh
- Computer Aided Drug Design and Molecular Modelling Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, Tamil Nadu, India
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6
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Loh YY, Anantharajan J, Huang Q, Xu W, Fulwood J, Ng HQ, Ng EY, Gea CY, Choong ML, Tan QW, Koh X, Lim WH, Nacro K, Cherian J, Baburajendran N, Ke Z, Kang C. Identification of small-molecule binding sites of a ubiquitin-conjugating enzyme-UBE2T through fragment-based screening. Protein Sci 2024; 33:e4904. [PMID: 38358126 PMCID: PMC10868430 DOI: 10.1002/pro.4904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 01/03/2024] [Accepted: 01/04/2024] [Indexed: 02/16/2024]
Abstract
UBE2T is an attractive target for drug development due to its linkage with several types of cancers. However, the druggability of ubiquitin-conjugating E2 (UBE2T) is low because of the lack of a deep and hydrophobic pocket capable of forming strong binding interactions with drug-like small molecules. Here, we performed fragment screening using 19 F-nuclear magnetic resonance (NMR) and validated the hits with 1 H-15 N-heteronuclear single quantum coherence (HSQC) experiment and X-ray crystallographic studies. The cocrystal structures obtained revealed the binding modes of the hit fragments and allowed for the characterization of the fragment-binding sites. Further screening of structural analogues resulted in the identification of a compound series with inhibitory effect on UBE2T activity. Our current study has identified two new binding pockets in UBE2T, which will be useful for the development of small molecules to regulate the function of this protein. In addition, the compounds identified in this study can serve as chemical starting points for the development of UBE2T modulators.
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Affiliation(s)
- Yong Yao Loh
- Experimental Drug Development Centre (EDDC)Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Jothi Anantharajan
- Experimental Drug Development Centre (EDDC)Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Qiwei Huang
- Experimental Drug Development Centre (EDDC)Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Weijun Xu
- Experimental Drug Development Centre (EDDC)Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Justina Fulwood
- Experimental Drug Development Centre (EDDC)Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Hui Qi Ng
- Experimental Drug Development Centre (EDDC)Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Elizabeth Yihui Ng
- Experimental Drug Development Centre (EDDC)Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Chong Yu Gea
- Experimental Drug Development Centre (EDDC)Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Meng Ling Choong
- Experimental Drug Development Centre (EDDC)Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Qian Wen Tan
- Experimental Drug Development Centre (EDDC)Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Xiaoying Koh
- Experimental Drug Development Centre (EDDC)Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Wan Hsin Lim
- Experimental Drug Development Centre (EDDC)Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Kassoum Nacro
- Experimental Drug Development Centre (EDDC)Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Joseph Cherian
- Experimental Drug Development Centre (EDDC)Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Nithya Baburajendran
- Experimental Drug Development Centre (EDDC)Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Zhiyuan Ke
- Experimental Drug Development Centre (EDDC)Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - CongBao Kang
- Experimental Drug Development Centre (EDDC)Agency for Science, Technology and Research (A*STAR)SingaporeSingapore
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7
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Srivastava V, Godara P, Jena SP, Naik B, Singh S, Prajapati VK, Prusty D. Peptide-ligand conjugate based immunotherapeutic approach for targeted dismissal of non-structural protein 1 of dengue virus: A novel therapeutic solution for mild and severe dengue infections. Int J Biol Macromol 2024; 260:129562. [PMID: 38246445 DOI: 10.1016/j.ijbiomac.2024.129562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 01/13/2024] [Accepted: 01/15/2024] [Indexed: 01/23/2024]
Abstract
Dengue virus infection has significantly increased, with reported cases soaring from 505,430 in 2000 to 2,809,818 in 2022, emphasizing the need for effective treatments. Among the eleven structural and non-structural proteins of DENV, Non-structural protein 1 (NS1) has emerged as a promising target due to its diverse role in modulating the immune response, inducing vascular leakage, and facilitating viral replication and assembly. Monoclonal antibodies are the sole therapeutics to target NS1, but concerns about their cross-reactivity persist. Given these concerns, our study focuses on designing a novel Peptide Ligand Conjugate (PLC) as a potential alternative immunotherapeutic agent against NS1. This PLC aims to mediate the immune elimination of soluble NS1 and NS1-presenting DENV-infected host cells by pre-existing vaccine-induced immunity. By employing the High Throughput Virtual Screening (HTVS) method, QikProp analysis, and Molecular Dynamics studies, we identified three hits from Asinex Biodesigned Ligands out of 220,177 compounds that show strong binding affinity towards the monoclonal binding site of NS1 protein. After a rigorous analysis of physicochemical characteristics, antigenicity, allergenicity, and toxicity using various servers, we selected two peptides: the minimum epitopic region of the Diphtheria and Tetanus toxins as the peptide components of the PLCs. A non-cleavable, non-reactive oxime linker connected the ligand with the peptide through oxime and amide bonds. DPT vaccine is widely used in dengue-endemic countries, and it has been reported that antibodies titer against MER of Diphtheria toxin and Tetanus toxins persist lifelong in DPT-vaccinated people. Therefore, once the rationally designed PLCs bind to NS1 through the ligands, the peptide will induce an immune response against NS1 by triggering pre-existing DPT antibodies and activating memory cells. This orchestrated immune response will destroy soluble NS1 and NS1-expressing DENV-infected cells, thereby reducing the illness of severe dengue hemorrhagic fever and the DENV infection, respectively. Given the increasing demand for new therapeutics for DENV treatment, further investigation into this novel immune-therapeutic strategy may offer a new avenue for treating mild and severe dengue infections.
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Affiliation(s)
- Varshita Srivastava
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Ajmer, 305817, India
| | - Priya Godara
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Ajmer, 305817, India
| | - Sudip Prasad Jena
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Ajmer, 305817, India
| | - Biswajit Naik
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Ajmer, 305817, India
| | - Satyendra Singh
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Ajmer, 305817, India
| | - Vijay Kumar Prajapati
- Department of Biochemistry, University of Delhi South Campus, Benito Juarez Road, Dhaula Kuan, New Delhi 110021, India
| | - Dhaneswar Prusty
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Ajmer, 305817, India.
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Martinsen E, Jinnurine T, Subramani S, Rogne M. Advances in RNA therapeutics for modulation of 'undruggable' targets. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 204:249-294. [PMID: 38458740 DOI: 10.1016/bs.pmbts.2023.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/10/2024]
Abstract
Over the past decades, drug discovery utilizing small pharmacological compounds, fragment-based therapeutics, and antibody therapy have significantly advanced treatment options for many human diseases. However, a major bottleneck has been that>70% of human proteins/genomic regions are 'undruggable' by the above-mentioned approaches. Many of these proteins constitute essential drug targets against complex multifactorial diseases like cancer, immunological disorders, and neurological diseases. Therefore, alternative approaches are required to target these proteins or genomic regions in human cells. RNA therapeutics is a promising approach for many of the traditionally 'undruggable' targets by utilizing methods such as antisense oligonucleotides, RNA interference, CRISPR/Cas-based genome editing, aptamers, and the development of mRNA therapeutics. In the following chapter, we will put emphasis on recent advancements utilizing these approaches against challenging drug targets, such as intranuclear proteins, intrinsically disordered proteins, untranslated genomic regions, and targets expressed in inaccessible tissues.
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Affiliation(s)
| | | | - Saranya Subramani
- Pioneer Research AS, Oslo Science Park, Oslo, Norway; Department of Pharmacy, Section for Pharmacology and Pharmaceutical Biosciences, University of Oslo, Oslo, Norway
| | - Marie Rogne
- Pioneer Research AS, Oslo Science Park, Oslo, Norway; Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway.
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9
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Xiao L, Xian M, Zhang C, Guo Q, Yi Q. Lipid peroxidation of immune cells in cancer. Front Immunol 2024; 14:1322746. [PMID: 38259464 PMCID: PMC10800824 DOI: 10.3389/fimmu.2023.1322746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 12/19/2023] [Indexed: 01/24/2024] Open
Abstract
Growing evidence indicates that cellular metabolism is a critical determinant of immune cell viability and function in antitumor immunity and lipid metabolism is important for immune cell activation and adaptation to the tumor microenvironment (TME). Lipid peroxidation is a process in which oxidants attack lipid-containing carbon-carbon double bonds and is an important part of lipid metabolism. In the past decades, studies have shown that lipid peroxidation participates in signal transduction to control cell proliferation, differentiation, and cell death, which is essential for cell function execution and human health. More importantly, recent studies have shown that lipid peroxidation affects immune cell function to modulate tumor immunity and antitumor ability. In this review, we briefly overview the effect of lipid peroxidation on the adaptive and innate immune cell activation and function in TME and discuss the effectiveness and sensitivity of the antitumor ability of immune cells by regulating lipid peroxidation.
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Affiliation(s)
| | | | | | | | - Qing Yi
- Center for Translational Research in Hematologic Malignancies, Houston Methodist Neal Cancer Center, Houston Methodist Research Institute, Houston Methodist, Houston, TX, United States
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10
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Alsolami ES, Alorfi HS, Alamry KA, Hussein MA. One-pot multicomponent polymerization towards heterocyclic polymers: a mini review. RSC Adv 2024; 14:1757-1781. [PMID: 38192311 PMCID: PMC10772543 DOI: 10.1039/d3ra07278a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 12/11/2023] [Indexed: 01/10/2024] Open
Abstract
Multicomponent polymerization (MCP) is an innovative field related to polymer-based chemistry that offers numerous advantages derived from multicomponent reactions (MCRs). One of the key advantages of MCP is its ability to achieve high efficiency. Additionally, MCP offers other advantages, including operational simplicity, mild reaction conditions, and atom economy. MCP is a versatile technique that is used for synthesizing a wide range of analogs from several classes of heterocyclic compounds. The ring structures of heterocyclic polymers give them different mechanical, photophysical, and electrical properties to other types of polymers. Because of their unique properties, heterocyclic polymers have been widely utilized in various significant applications. MCRs are a type of chemical reaction that can be used to synthesize a wide variety of compounds in a single pot, which allows researchers to quickly assemble libraries of compounds. The development of MCPs from MCRs has made it easier to access a library of polymers with tunable structures. However, MCPs related to alkynes or acetylene triple bonds have more potential. In this review study, we provide an overview of the synthesis of heteroatom-functional polymers and alkyne-based development or other reactions such as Cu-catalyzed, catalyst-free, MCCP, MCTPs, green monomers, A3 coupling reactions, Passerini reactions, and sequence- and controlled-multicomponent polymerization. The up-to-date progress provides a convenient and efficient kind of approach related to heteroatoms and MCP synthesis, and perspectives in terms of future directions are also discussed in the study.
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Affiliation(s)
- Eman S Alsolami
- Chemistry Department, Faculty of Science, King Abdulaziz University P. O. Box 80203 Jeddah 21589 Saudi Arabia
| | - Hajar S Alorfi
- Chemistry Department, Faculty of Science, King Abdulaziz University P. O. Box 80203 Jeddah 21589 Saudi Arabia
| | - Khalid A Alamry
- Chemistry Department, Faculty of Science, King Abdulaziz University P. O. Box 80203 Jeddah 21589 Saudi Arabia
| | - Mahmoud A Hussein
- Chemistry Department, Faculty of Science, King Abdulaziz University P. O. Box 80203 Jeddah 21589 Saudi Arabia
- Chemistry Department, Faculty of Science, Assiut University Assiut 71516 Egypt
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11
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Monfared N, Gold M, Carbery I, Laube R, Selinger CP. Reproductive Safety Issues of Novel Small Molecules for the Treatment of Inflammatory Bowel Disease: A Systematic Review. J Clin Med 2023; 13:34. [PMID: 38202041 PMCID: PMC10780022 DOI: 10.3390/jcm13010034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 12/08/2023] [Accepted: 12/18/2023] [Indexed: 01/12/2024] Open
Abstract
Maintenance of remission during pregnancy is vital for women with inflammatory bowel disease (IBD). The antenatal safety of novel small molecules for IBD is yet to be ascertained. We aimed to describe the current evidence on reproductive data regarding small-molecule drugs. We performed a systematic review searching Embase Classic + Embase and Ovid MEDLINE for reproductive outcomes for tofacitinib, filgotinib, upadacitininb, and ozanimod. Additionally, we asked the manufacturers for available data on file regarding reproduction. We analysed data from 10 sources; six studies and four manufacturer reports were identified from our search. Significant malformation risks were reported for tofacitinib, filgotinib, upadacitininb, and ozanimod in animal studies. In 126 tofacitinib-exposed pregnancies, there were 55 live births with 2 congenital malformations and 1 serious infant infection, 14 terminations, 15 miscarriages, and 42 outcomes unknown. In 50 filgotinib-exposed pregnancies, there were 20 healthy babies, 1 congenital malformation, 9 terminations, 10 miscarriages, and 10 outcomes unknown. In 78 upadacitinib-exposed pregnancies, there were 30 healthy babies, 15 terminations, 15 miscarriages, and 18 outcomes unknown. In 60 ozanimod-exposed pregnancies, there were 31 live births with 1 congenital malformation, 1 case of intra-uterine growth restriction, 1 case of neonatal icterus, 13 terminations, 9 miscarriages, and 8 unknown outcomes. Animal data suggest significant risks of malformations for tofacitinib, filgotinib, upadacitininb, and ozanimod. Human data from clinical trials and real-world observations do not show concerning data so far, but these are very limited. Currently, alternative treatments should be used for IBD during pregnancy.
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Affiliation(s)
| | | | | | | | - Christian P. Selinger
- Leeds Gastroenterology Institute, Leeds Teaching Hospitals, Leeds LS9 7TF, UK; (N.M.); (M.G.); (R.L.)
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12
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Kosonocky CW, Wilke CO, Marcotte EM, Ellington AD. Mining Patents with Large Language Models Elucidates the Chemical Function Landscape. ARXIV 2023:arXiv:2309.08765v2. [PMID: 38196747 PMCID: PMC10775343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
The fundamental goal of small molecule discovery is to generate chemicals with target functionality. While this often proceeds through structure-based methods, we set out to investigate the practicality of orthogonal methods that leverage the extensive corpus of chemical literature. We hypothesize that a sufficiently large text-derived chemical function dataset would mirror the actual landscape of chemical functionality. Such a landscape would implicitly capture complex physical and biological interactions given that chemical function arises from both a molecule's structure and its interacting partners. To evaluate this hypothesis, we built a Chemical Function (CheF) dataset of patent-derived functional labels. This dataset, comprising 631K molecule-function pairs, was created using an LLM- and embedding-based method to obtain functional labels for approximately 100K molecules from their corresponding 188K unique patents. We carry out a series of analyses demonstrating that the CheF dataset contains a semantically coherent textual representation of the functional landscape congruent with chemical structural relationships, thus approximating the actual chemical function landscape. We then demonstrate that this text-based functional landscape can be leveraged to identify drugs with target functionality using a model able to predict functional profiles from structure alone. We believe that functional label-guided molecular discovery may serve as an orthogonal approach to traditional structure-based methods in the pursuit of designing novel functional molecules.
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13
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De la Rosa MVG, Patel D, McCann MR, Stringer KA, Rosania GR. Database screening as a strategy to identify endogenous candidate metabolites to probe and assess mitochondrial drug toxicity. Sci Rep 2023; 13:22013. [PMID: 38086883 PMCID: PMC10716408 DOI: 10.1038/s41598-023-49443-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 12/08/2023] [Indexed: 12/18/2023] Open
Abstract
Adverse drug reactions (ADRs) are considered an inherent risk of medication use, and some ADRs have been associated with off-target drug interactions with mitochondria. Metabolites that reflect mitochondrial function may help identify patients at risk of mitochondrial toxicity. We employed a database strategy to identify candidate mitochondrial metabolites that could be clinically useful to identify individuals at increased risk of mitochondrial-related ADRs. This led to L-carnitine being identified as the candidate mitochondrial metabolite. L-carnitine, its acetylated metabolite, acetylcarnitine and other acylcarnitines are mitochondrial biomarkers used to detect inborn errors of metabolism. We hypothesized that changes in L-carnitine disposition, induced by a "challenge test" of intravenous L-carnitine, could identify mitochondrial-related ADRs by provoking variation in L-carnitine and/or acetylcarnitine blood levels. To test this hypothesis, we induced mitochondrial drug toxicity with clofazimine (CFZ) in a mouse model. Following CFZ treatment, mice received an L-carnitine "challenge test". CFZ-induced changes in weight were consistent with previous work and reflect CFZ-induced catabolism. L-carnitine induced differences in whole blood acetylcarnitine concentrations in a manner that was dependent on CFZ treatment. This supports the usefulness of a database strategy for the discovery of candidate metabolite biomarkers of drug toxicity and substantiates the potential of the L-carnitine "challenge test" as a "probe" to identify drug-related toxicological manifestations.
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Affiliation(s)
- Mery Vet George De la Rosa
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, Ann Arbor, MI, 48104, USA
| | - Dipali Patel
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, Ann Arbor, MI, 48104, USA
| | - Marc R McCann
- The NMR Metabolomics Laboratory, Department of Clinical Pharmacy, College of Pharmacy, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Kathleen A Stringer
- The NMR Metabolomics Laboratory, Department of Clinical Pharmacy, College of Pharmacy, University of Michigan, Ann Arbor, MI, 48109, USA
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, School of Medicine, University of Michigan, Ann Arbor, MI, 48109, USA
- Weil Institute for Critical Care Research and Innovation, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Gus R Rosania
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, Ann Arbor, MI, 48104, USA.
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14
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Kosonocky CW, Feller AL, Wilke CO, Ellington AD. Using alternative SMILES representations to identify novel functional analogues in chemical similarity vector searches. PATTERNS (NEW YORK, N.Y.) 2023; 4:100865. [PMID: 38106612 PMCID: PMC10724362 DOI: 10.1016/j.patter.2023.100865] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 08/09/2023] [Accepted: 10/06/2023] [Indexed: 12/19/2023]
Abstract
Chemical similarity searches are a widely used family of in silico methods for identifying pharmaceutical leads. These methods historically relied on structure-based comparisons to compute similarity. Here, we use a chemical language model to create a vector-based chemical search. We extend previous implementations by creating a prompt engineering strategy that utilizes two different chemical string representation algorithms: one for the query and the other for the database. We explore this method by reviewing search results from nine queries with diverse targets. We find that the method identifies molecules with similar patent-derived functionality to the query, as determined by our validated LLM-assisted patent summarization pipeline. Further, many of these functionally similar molecules have different structures and scaffolds from the query, making them unlikely to be found with traditional chemical similarity searches. This method may serve as a new tool for the discovery of novel molecular structural classes that achieve target functionality.
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Affiliation(s)
- Clayton W. Kosonocky
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78705, USA
| | - Aaron L. Feller
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78705, USA
| | - Claus O. Wilke
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78705, USA
| | - Andrew D. Ellington
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78705, USA
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX 78705, USA
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15
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Talukdar PD, Chatterji U. Transcriptional co-activators: emerging roles in signaling pathways and potential therapeutic targets for diseases. Signal Transduct Target Ther 2023; 8:427. [PMID: 37953273 PMCID: PMC10641101 DOI: 10.1038/s41392-023-01651-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: 04/18/2023] [Revised: 08/27/2023] [Accepted: 09/10/2023] [Indexed: 11/14/2023] Open
Abstract
Specific cell states in metazoans are established by the symphony of gene expression programs that necessitate intricate synergic interactions between transcription factors and the co-activators. Deregulation of these regulatory molecules is associated with cell state transitions, which in turn is accountable for diverse maladies, including developmental disorders, metabolic disorders, and most significantly, cancer. A decade back most transcription factors, the key enablers of disease development, were historically viewed as 'undruggable'; however, in the intervening years, a wealth of literature validated that they can be targeted indirectly through transcriptional co-activators, their confederates in various physiological and molecular processes. These co-activators, along with transcription factors, have the ability to initiate and modulate transcription of diverse genes necessary for normal physiological functions, whereby, deregulation of such interactions may foster tissue-specific disease phenotype. Hence, it is essential to analyze how these co-activators modulate specific multilateral processes in coordination with other factors. The proposed review attempts to elaborate an in-depth account of the transcription co-activators, their involvement in transcription regulation, and context-specific contributions to pathophysiological conditions. This review also addresses an issue that has not been dealt with in a comprehensive manner and hopes to direct attention towards future research that will encompass patient-friendly therapeutic strategies, where drugs targeting co-activators will have enhanced benefits and reduced side effects. Additional insights into currently available therapeutic interventions and the associated constraints will eventually reveal multitudes of advanced therapeutic targets aiming for disease amelioration and good patient prognosis.
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Affiliation(s)
- Priyanka Dey Talukdar
- Cancer Research Laboratory, Department of Zoology, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, 700019, West Bengal, India
| | - Urmi Chatterji
- Cancer Research Laboratory, Department of Zoology, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, 700019, West Bengal, India.
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16
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Hua L, Wang D, Wang K, Wang Y, Gu J, Zhang Q, You Q, Wang L. Design of Tracers in Fluorescence Polarization Assay for Extensive Application in Small Molecule Drug Discovery. J Med Chem 2023; 66:10934-10958. [PMID: 37561645 DOI: 10.1021/acs.jmedchem.3c00881] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2023]
Abstract
Development of fluorescence polarization (FP) assays, especially in a competitive manner, is a potent and mature tool for measuring the binding affinities of small molecules. This approach is suitable for high-throughput screening (HTS) for initial ligands and is also applicable for further study of the structure-activity relationships (SARs) of candidate compounds for drug discovery. Buffer and tracer, especially rational design of the tracer, play a vital role in an FP assay system. In this perspective, we provided different kinds of approaches for tracer design based on successful cases in recent years. We classified these tracers by different types of ligands in tracers, including peptide, nucleic acid, natural product, and small molecule. To make this technology accessible for more targets, we briefly described the basic theory and workflow, followed by highlighting the design and application of typical FP tracers from a perspective of medicinal chemistry.
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Affiliation(s)
- Liwen Hua
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Danni Wang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Keran Wang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Yuxuan Wang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Jinying Gu
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Qiuyue Zhang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Qidong You
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Lei Wang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
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17
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Nguyen NPK, Tran KN, Nguyen LTH, Shin HM, Yang IJ. Effects of Essential Oils and Fragrant Compounds on Appetite: A Systematic Review. Int J Mol Sci 2023; 24:ijms24097962. [PMID: 37175666 PMCID: PMC10178777 DOI: 10.3390/ijms24097962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/21/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023] Open
Abstract
Appetite dysregulation is one of the factors contributing to anorexia, bulimia nervosa, obesity, and diabetes. Essential oils or fragrant compounds have been proven to regulate food intake and energy expenditure; hence, this study aimed to summarize their effects on appetite and the underlying mechanisms. The PubMed and Web of Science databases were searched until July 2022. Only two of the 41 studies were performed clinically, and the remaining 39 used animal models. Oral administration was the most common route, and a dosage range of 100-2000 mg/kg for mice or 2-32 mg/kg for rats was applied, with a duration of 12 days to 4 weeks, followed by inhalation (10-6-10-3 mg/cage or 10-9-10-2 mg/cm3 within 1 h). Approximately 11 essential oil samples and 22 fragrant compounds were found to increase appetite, while 12 essential oils and seven compounds decreased appetite. These fragrant components can exert appetite-regulating effects via leptin resistance, the activity of sympathetic/parasympathetic nerves, or the mRNA expression of neuropeptide Y (NPY)/agouti-related protein (AgRP), cocaine- and amphetamine-regulated transcript (CART)/proopiomelanocortin (POMC) in the hypothalamus. Fragrance memory and cognitive processes may also play roles in appetite regulation. The findings of this study accentuate the potential of essential oils and fragrant compounds to regulate appetite and eating disorders.
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Affiliation(s)
- Nhi Phuc Khanh Nguyen
- Department of Physiology, College of Korean Medicine, Dongguk University, Gyeongju 38066, Republic of Korea
| | - Khoa Nguyen Tran
- Department of Physiology, College of Korean Medicine, Dongguk University, Gyeongju 38066, Republic of Korea
| | - Ly Thi Huong Nguyen
- Department of Physiology, College of Korean Medicine, Dongguk University, Gyeongju 38066, Republic of Korea
| | - Heung-Mook Shin
- Department of Physiology, College of Korean Medicine, Dongguk University, Gyeongju 38066, Republic of Korea
| | - In-Jun Yang
- Department of Physiology, College of Korean Medicine, Dongguk University, Gyeongju 38066, Republic of Korea
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18
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Greco A, Laudani C, Spagnolo M, Agnello F, Faro DC, Finocchiaro S, Legnazzi M, Mauro MS, Mazzone PM, Occhipinti G, Rochira C, Scalia L, Capodanno D. Pharmacology and Clinical Development of Factor XI Inhibitors. Circulation 2023; 147:897-913. [PMID: 36913497 DOI: 10.1161/circulationaha.122.062353] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/14/2023]
Abstract
Therapeutic anticoagulation is indicated for a variety of circumstances and conditions in several fields of medicine to prevent or treat venous and arterial thromboembolism. According to the different mechanisms of action, the available parenteral and oral anticoagulant drugs share the common principle of hampering or blocking key steps of the coagulation cascade, which unavoidably comes at the price of an increased propensity to bleed. Hemorrhagic complications affect patient prognosis both directly and indirectly (ie, by preventing the adoption of an effective antithrombotic strategy). Inhibition of factor XI (FXI) has emerged as a strategy with the potential to uncouple the pharmacological effect and the adverse events of anticoagulant therapy. This observation is based on the differential contribution of FXI to thrombus amplification, in which it plays a major role, and hemostasis, in which it plays an ancillary role in final clot consolidation. Several agents were developed to inhibit FXI at different stages (ie, suppressing biosynthesis, preventing zymogen activation, or impeding the biological action of the active form), including antisense oligonucleotides, monoclonal antibodies, small synthetic molecules, natural peptides, and aptamers. Phase 2 studies of different classes of FXI inhibitors in orthopedic surgery suggested that dose-dependent reductions in thrombotic complications are not paralleled by dose-dependent increases in bleeding compared with low-molecular-weight heparin. Likewise, the FXI inhibitor asundexian was associated with lower rates of bleeding compared with the activated factor X inhibitor apixaban in patients with atrial fibrillation, although no evidence of a therapeutic effect on stroke prevention is available so far. FXI inhibition could also be appealing for patients with other conditions, including end-stage renal disease, noncardioembolic stroke, or acute myocardial infarction, for which other phase 2 studies have been conducted. The balance between thromboprophylaxis and bleeding achieved by FXI inhibitors needs confirmation in large-scale phase 3 clinical trials powered for clinical end points. Several of such trials are ongoing or planned to define the role of FXI inhibitors in clinical practice and to clarify which FXI inhibitor may be most suited for each clinical indication. This article reviews the rationale, pharmacology, results of medium or small phase 2 studies, and future perspectives of drugs inhibiting FXI.
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Affiliation(s)
- Antonio Greco
- A.O.U. Policlinico "G. Rodolico - San Marco", University of Catania, Italy
| | - Claudio Laudani
- A.O.U. Policlinico "G. Rodolico - San Marco", University of Catania, Italy
| | - Marco Spagnolo
- A.O.U. Policlinico "G. Rodolico - San Marco", University of Catania, Italy
| | - Federica Agnello
- A.O.U. Policlinico "G. Rodolico - San Marco", University of Catania, Italy
| | | | - Simone Finocchiaro
- A.O.U. Policlinico "G. Rodolico - San Marco", University of Catania, Italy
| | - Marco Legnazzi
- A.O.U. Policlinico "G. Rodolico - San Marco", University of Catania, Italy
| | - Maria Sara Mauro
- A.O.U. Policlinico "G. Rodolico - San Marco", University of Catania, Italy
| | | | | | - Carla Rochira
- A.O.U. Policlinico "G. Rodolico - San Marco", University of Catania, Italy
| | - Lorenzo Scalia
- A.O.U. Policlinico "G. Rodolico - San Marco", University of Catania, Italy
| | - Davide Capodanno
- A.O.U. Policlinico "G. Rodolico - San Marco", University of Catania, Italy
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19
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Bąchor U, Junka A, Brożyna M, Mączyński M. The In Vitro Impact of Isoxazole Derivatives on Pathogenic Biofilm and Cytotoxicity of Fibroblast Cell Line. Int J Mol Sci 2023; 24:2997. [PMID: 36769319 PMCID: PMC9917413 DOI: 10.3390/ijms24032997] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/24/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
The microbial, biofilm-based infections of chronic wounds are one of the major challenges of contemporary medicine. The use of topically administered antiseptic agents is essential to treat wound-infecting microorganisms. Due to observed microbial tolerance/resistance against specific clinically-used antiseptics, the search for new, efficient agents is of pivotal meaning. Therefore, in this work, 15 isoxazole derivatives were scrutinized against leading biofilm wound pathogens Staphylococcus aureus and Pseudomonas aeruginosa, and against Candida albicans fungus. For this purpose, the minimal inhibitory concentration, biofilm reduction in microtitrate plates, modified disk diffusion methods and antibiofilm dressing activity measurement methods were applied. Moreover, the cytotoxicity and cytocompatibility of derivatives was tested toward wound bed-forming cells, referred to as fibroblasts, using normative methods. Obtained results revealed that all isoxazole derivatives displayed antimicrobial activity and low cytotoxic effect, but antimicrobial activity of two derivatives, 2-(cyclohexylamino)-1-(5-nitrothiophen-2-yl)-2-oxoethyl 5-amino-3-methyl-1,2-oxazole-4-carboxylate (PUB9) and 2-(benzylamino)-1-(5-nitrothiophen-2-yl)-2-oxoethyl 5-amino-3-methyl-1,2-oxazole-4-carboxylate (PUB10), was noticeably higher compared to the other compounds analyzed, especially PUB9 with regard to Staphylococcus aureus, with a minimal inhibitory concentration more than x1000 lower compared to the remaining derivatives. The PUB9 and PUB10 derivatives were able to reduce more than 90% of biofilm-forming cells, regardless of the species, displaying at the same time none (PUB9) or moderate (PUB10) cytotoxicity against fibroblasts and high (PUB9) or moderate (PUB10) cytocompatibility against these wound cells. Therefore, taking into consideration the clinical demand for new antiseptic agents for non-healing wound treatment, PUB9 seems to be a promising candidate to be further tested in advanced animal models and later, if satisfactory results are obtained, in the clinical setting.
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Affiliation(s)
- Urszula Bąchor
- Department of Organic Chemistry and Drug Technology, Faculty of Pharmacy, Wroclaw Medical University, 50-556 Wroclaw, Poland
| | - Adam Junka
- Unique Application Model Laboratory, Department of Pharmaceutical Microbiology and Parasitology, Faculty of Pharmacy, Wroclaw Medical University, 50-556 Wroclaw, Poland
| | - Malwina Brożyna
- Unique Application Model Laboratory, Department of Pharmaceutical Microbiology and Parasitology, Faculty of Pharmacy, Wroclaw Medical University, 50-556 Wroclaw, Poland
| | - Marcin Mączyński
- Department of Organic Chemistry and Drug Technology, Faculty of Pharmacy, Wroclaw Medical University, 50-556 Wroclaw, Poland
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20
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Antimicrobial Resistance and Recent Alternatives to Antibiotics for the Control of Bacterial Pathogens with an Emphasis on Foodborne Pathogens. Antibiotics (Basel) 2023; 12:antibiotics12020274. [PMID: 36830185 PMCID: PMC9952301 DOI: 10.3390/antibiotics12020274] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 01/21/2023] [Accepted: 01/27/2023] [Indexed: 01/31/2023] Open
Abstract
Antimicrobial resistance (AMR) is one of the most important global public health problems. The imprudent use of antibiotics in humans and animals has resulted in the emergence of antibiotic-resistant bacteria. The dissemination of these strains and their resistant determinants could endanger antibiotic efficacy. Therefore, there is an urgent need to identify and develop novel strategies to combat antibiotic resistance. This review provides insights into the evolution and the mechanisms of AMR. Additionally, it discusses alternative approaches that might be used to control AMR, including probiotics, prebiotics, antimicrobial peptides, small molecules, organic acids, essential oils, bacteriophage, fecal transplants, and nanoparticles.
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21
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Taha-Abdelaziz K, Singh M, Sharif S, Sharma S, Kulkarni RR, Alizadeh M, Yitbarek A, Helmy YA. Intervention Strategies to Control Campylobacter at Different Stages of the Food Chain. Microorganisms 2023; 11:microorganisms11010113. [PMID: 36677405 PMCID: PMC9866650 DOI: 10.3390/microorganisms11010113] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 12/16/2022] [Accepted: 12/28/2022] [Indexed: 01/04/2023] Open
Abstract
Campylobacter is one of the most common bacterial pathogens of food safety concern. Campylobacter jejuni infects chickens by 2-3 weeks of age and colonized chickens carry a high C. jejuni load in their gut without developing clinical disease. Contamination of meat products by gut contents is difficult to prevent because of the high numbers of C. jejuni in the gut, and the large percentage of birds infected. Therefore, effective intervention strategies to limit human infections of C. jejuni should prioritize the control of pathogen transmission along the food supply chain. To this end, there have been ongoing efforts to develop innovative ways to control foodborne pathogens in poultry to meet the growing customers' demand for poultry meat that is free of foodborne pathogens. In this review, we discuss various approaches that are being undertaken to reduce Campylobacter load in live chickens (pre-harvest) and in carcasses (post-harvest). We also provide some insights into optimization of these approaches, which could potentially help improve the pre- and post-harvest practices for better control of Campylobacter.
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Affiliation(s)
- Khaled Taha-Abdelaziz
- Department of Animal and Veterinary Science, College of Agriculture, Forestry and Life Sciences, Clemson University, Clemson, SC 29634, USA
- Correspondence:
| | - Mankerat Singh
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Shayan Sharif
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Shreeya Sharma
- Department of Animal and Veterinary Science, College of Agriculture, Forestry and Life Sciences, Clemson University, Clemson, SC 29634, USA
| | - Raveendra R. Kulkarni
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27606, USA
| | - Mohammadali Alizadeh
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Alexander Yitbarek
- Department of Animal Science, McGill University, Montreal, QC H9X 3V9, Canada
| | - Yosra A. Helmy
- Department of Veterinary Science, College of Agriculture, Food, and Environment, University of Kentucky, Lexington, KY 40546, USA
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22
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Chen J, Chen Z, Chen R, Feng D, Li T, Han H, Bi X, Wang Z, Li K, Li Y, Li X, Wang L, Li J. HCDT: an integrated highly confident drug-target resource. Database (Oxford) 2022; 2022:6843794. [PMID: 36420558 PMCID: PMC9684616 DOI: 10.1093/database/baac101] [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: 07/29/2022] [Revised: 10/12/2022] [Accepted: 11/01/2022] [Indexed: 11/25/2022]
Abstract
Drug-target association plays an important role in drug discovery, drug repositioning, drug synergy prediction, etc. Currently, a lot of drug-related databases, such as DrugBank and BindingDB, have emerged. However, these databases are separate, incomplete and non-uniform with different criteria. Here, we integrated eight drug-related databases; collected, filtered and supplemented drugs, target genes and experimentally validated (highly confident) associations and built a highly confident drug-target (HCDT: http://hainmu-biobigdata.com/hcdt) database. HCDT database includes 500 681 HCDT associations between 299 458 drugs and 5618 target genes. Compared to individual databases, HCDT database contains 1.1 to 254.2 times drugs, 1.8-5.5 times target genes and 1.4-27.7 times drug-target associations. It is normative, publicly available and easy for searching, browsing and downloading. Together with multi-omics data, it will be a good resource in analyzing the drug functional mechanism, mining drug-related biological pathways, predicting drug synergy, etc. Database URL: http://hainmu-biobigdata.com/hcdt.
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Affiliation(s)
| | | | - Rufei Chen
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Bioinformatics for Major Diseases Science Innovation Group, College of Biomedical Informatics and Engineering, Hainan Medical University, Haikou 571199, China
| | - Dehua Feng
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Bioinformatics for Major Diseases Science Innovation Group, College of Biomedical Informatics and Engineering, Hainan Medical University, Haikou 571199, China
| | - Tianyi Li
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Bioinformatics for Major Diseases Science Innovation Group, College of Biomedical Informatics and Engineering, Hainan Medical University, Haikou 571199, China
| | - Huirui Han
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Bioinformatics for Major Diseases Science Innovation Group, College of Biomedical Informatics and Engineering, Hainan Medical University, Haikou 571199, China
| | - Xiaoman Bi
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Bioinformatics for Major Diseases Science Innovation Group, College of Biomedical Informatics and Engineering, Hainan Medical University, Haikou 571199, China
| | - Zhenzhen Wang
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Bioinformatics for Major Diseases Science Innovation Group, College of Biomedical Informatics and Engineering, Hainan Medical University, Haikou 571199, China
| | - Kongning Li
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Bioinformatics for Major Diseases Science Innovation Group, College of Biomedical Informatics and Engineering, Hainan Medical University, Haikou 571199, China
| | - Yongsheng Li
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Bioinformatics for Major Diseases Science Innovation Group, College of Biomedical Informatics and Engineering, Hainan Medical University, Haikou 571199, China
| | - Xia Li
- *Corresponding author: Tel: +86-451-86615922; Fax: +86-451-86615922; Correspondence may also be addressed to Limei Wang. Tel: +86-898-66893770; Fax: +86-898-66893770; and Jin Li. Tel: +86-898-66893770; Fax: +86-898-66893770;
| | - Limei Wang
- *Corresponding author: Tel: +86-451-86615922; Fax: +86-451-86615922; Correspondence may also be addressed to Limei Wang. Tel: +86-898-66893770; Fax: +86-898-66893770; and Jin Li. Tel: +86-898-66893770; Fax: +86-898-66893770;
| | - Jin Li
- *Corresponding author: Tel: +86-451-86615922; Fax: +86-451-86615922; Correspondence may also be addressed to Limei Wang. Tel: +86-898-66893770; Fax: +86-898-66893770; and Jin Li. Tel: +86-898-66893770; Fax: +86-898-66893770;
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23
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Doolan JA, Williams GT, Hilton KLF, Chaudhari R, Fossey JS, Goult BT, Hiscock JR. Advancements in antimicrobial nanoscale materials and self-assembling systems. Chem Soc Rev 2022; 51:8696-8755. [PMID: 36190355 PMCID: PMC9575517 DOI: 10.1039/d1cs00915j] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Indexed: 11/21/2022]
Abstract
Antimicrobial resistance is directly responsible for more deaths per year than either HIV/AIDS or malaria and is predicted to incur a cumulative societal financial burden of at least $100 trillion between 2014 and 2050. Already heralded as one of the greatest threats to human health, the onset of the coronavirus pandemic has accelerated the prevalence of antimicrobial resistant bacterial infections due to factors including increased global antibiotic/antimicrobial use. Thus an urgent need for novel therapeutics to combat what some have termed the 'silent pandemic' is evident. This review acts as a repository of research and an overview of the novel therapeutic strategies being developed to overcome antimicrobial resistance, with a focus on self-assembling systems and nanoscale materials. The fundamental mechanisms of action, as well as the key advantages and disadvantages of each system are discussed, and attention is drawn to key examples within each field. As a result, this review provides a guide to the further design and development of antimicrobial systems, and outlines the interdisciplinary techniques required to translate this fundamental research towards the clinic.
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Affiliation(s)
- Jack A Doolan
- School of Chemistry and Forensic Science, University of Kent, Canterbury, Kent CT2 7NH, UK.
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK.
| | - George T Williams
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
| | - Kira L F Hilton
- School of Chemistry and Forensic Science, University of Kent, Canterbury, Kent CT2 7NH, UK.
| | - Rajas Chaudhari
- School of Chemistry and Forensic Science, University of Kent, Canterbury, Kent CT2 7NH, UK.
| | - John S Fossey
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
| | - Benjamin T Goult
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK.
| | - Jennifer R Hiscock
- School of Chemistry and Forensic Science, University of Kent, Canterbury, Kent CT2 7NH, UK.
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24
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Li Q, Kang C. Dengue virus NS4B protein as a target for developing antivirals. Front Cell Infect Microbiol 2022; 12:959727. [PMID: 36017362 PMCID: PMC9398000 DOI: 10.3389/fcimb.2022.959727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 07/21/2022] [Indexed: 12/04/2022] Open
Abstract
Dengue virus is an important pathogen affecting global population while no specific treatment is available against this virus. Effort has been made to develop inhibitors through targeting viral nonstructural proteins such as NS3 and NS5 with enzymatic activities. No potent inhibitors entering clinical studies have been developed so far due to many challenges. The genome of dengue virus encodes four membrane-bound nonstructural proteins which do not possess any enzymatic activities. Studies have shown that the membrane protein-NS4B is a validated target for drug discovery and several NS4B inhibitors exhibited antiviral activities in various assays and entered preclinical studies.. Here, we summarize the recent studies on dengue NS4B protein. The structure and membrane topology of dengue NS4B derived from biochemical and biophysical studies are described. Function of NS4B through protein-protein interactions and some available NS4B inhibitors are summarized. Accumulated studies demonstrated that cell-based assays play important roles in developing NS4B inhibitors. Although the atomic structure of NS4B is not obtained, target-based drug discovery approach become feasible to develop NS4B inhibitors as recombinant NS4B protein is available.
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Affiliation(s)
- Qingxin Li
- Guangdong Provincial Engineering Laboratory of Biomass High Value Utilization, Institute of Biological and Medical Engineering, Guangdong Academy of Sciences, Guangzhou, China
- *Correspondence: Qingxin Li, ; Congbao Kang,
| | - Congbao Kang
- Experimental Drug Development Centre, Agency for Science, Technology and Research, Singapore, Singapore
- *Correspondence: Qingxin Li, ; Congbao Kang,
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25
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Yang Y, He J, Jiang Z, Du X, Chen F, Wang J, Ni H. Characterization of the inhibition of aldose reductase with
p
‐coumaric acid ethyl ester. J Food Biochem 2022; 46:e14370. [DOI: 10.1111/jfbc.14370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 06/14/2022] [Accepted: 07/22/2022] [Indexed: 12/01/2022]
Affiliation(s)
- Yuanfan Yang
- College of Ocean Food and Biological Engineering Jimei University Xiamen China
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering Xiamen China
- Research Center of Food Biotechnology of Xiamen City Xiamen China
| | - Junzhu He
- College of Ocean Food and Biological Engineering Jimei University Xiamen China
| | - Zedong Jiang
- College of Ocean Food and Biological Engineering Jimei University Xiamen China
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering Xiamen China
- Research Center of Food Biotechnology of Xiamen City Xiamen China
| | - Xiping Du
- College of Ocean Food and Biological Engineering Jimei University Xiamen China
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering Xiamen China
- Research Center of Food Biotechnology of Xiamen City Xiamen China
| | - Feng Chen
- Department of Food, Nutrition and Packaging Sciences Clemson University Clemson South Carolina USA
| | - Jinling Wang
- School of Forestry Northeast Forestry University Harbin China
| | - Hui Ni
- College of Ocean Food and Biological Engineering Jimei University Xiamen China
- Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering Xiamen China
- Research Center of Food Biotechnology of Xiamen City Xiamen China
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26
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Scope of repurposed drugs against the potential targets of the latest variants of SARS-CoV-2. Struct Chem 2022; 33:1585-1608. [PMID: 35938064 PMCID: PMC9346052 DOI: 10.1007/s11224-022-02020-z] [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: 04/18/2022] [Accepted: 07/19/2022] [Indexed: 11/21/2022]
Abstract
The unprecedented outbreak of the severe acute respiratory syndrome (SARS) Coronavirus-2, across the globe, triggered a worldwide uproar in the search for immediate treatment strategies. With no specific drug and not much data available, alternative approaches such as drug repurposing came to the limelight. To date, extensive research on the repositioning of drugs has led to the identification of numerous drugs against various important protein targets of the coronavirus strains, with hopes of the drugs working against the major variants of concerns (alpha, beta, gamma, delta, omicron) of the virus. Advancements in computational sciences have led to improved scope of repurposing via techniques such as structure-based approaches including molecular docking, molecular dynamic simulations and quantitative structure activity relationships, network-based approaches, and artificial intelligence-based approaches with other core machine and deep learning algorithms. This review highlights the various approaches to repurposing drugs from a computational biological perspective, with various mechanisms of action of the drugs against some of the major protein targets of SARS-CoV-2. Additionally, clinical trials data on potential COVID-19 repurposed drugs are also highlighted with stress on the major SARS-CoV-2 targets and the structural effect of variants on these targets. The interaction modelling of some important repurposed drugs has also been elucidated. Furthermore, the merits and demerits of drug repurposing are also discussed, with a focus on the scope and applications of the latest advancements in repurposing.
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27
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Duan X, Zhang L, Si H, Song J, Wang P, Chen S, Luo H, Rao X, Wang Z, Liao S. Synthesis, Antifungal Activity, Cytotoxicity and QSAR Study of Camphor Derivatives. J Fungi (Basel) 2022; 8:jof8080762. [PMID: 35893130 PMCID: PMC9332567 DOI: 10.3390/jof8080762] [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: 06/14/2022] [Revised: 07/19/2022] [Accepted: 07/20/2022] [Indexed: 12/10/2022] Open
Abstract
Control of fungal phytopathogens affecting crops and woodlands is an important goal in environmental management and the maintenance of food security. This work describes the synthesis of 37 camphor derivatives, of which 27 were new compounds. Their antifungal effects on six fungi were evaluated in vitro. Compounds 3a, 4a and 5k showed strong antifungal activity against Trametes versicolor, with EC50 values of 0.43, 6.80 and 4.86 mg/L, respectively, which were better than that of tricyclazole (EC50 118.20 mg/L) and close to or better than that of carbendazim (EC50 1.20 mg/L). The most potent compound, 3a, exhibited broad-spectrum antifungal activity towards six fungi with EC50 values within the range of 0.43–40.18 mg/L. Scanning electron microscopy demonstrated that compounds 3a, 4a and 5k gave irregular growth and shriveling of the mycelia. In vitro cytotoxicity evaluation revealed that the tested camphor derivatives had mild or no cytotoxicity for LO2 and HEK293T cell lines. Quantitative structure−activity relationship (QSAR) analysis revealed that the number of F atoms, relative molecular weight, the atomic orbital electronic population and total charge on the positively charged surfaces of the molecules of camphor derivatives have effects on antifungal activity. The present study may provide a theoretical basis for a high-value use of camphor and could be helpful for the development of novel potential antifungals.
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Affiliation(s)
- Xinying Duan
- East China Woody Fragrance and Flavor Engineering Research Center of National Forestry and Grassland Administration, Camphor Engineering Research Center of National Forestry and Grassland Administration, College of Forestry, Jiangxi Agricultural University, Nanchang 330045, China; (X.D.); (L.Z.); (H.S.); (P.W.); (S.C.); (H.L.)
| | - Li Zhang
- East China Woody Fragrance and Flavor Engineering Research Center of National Forestry and Grassland Administration, Camphor Engineering Research Center of National Forestry and Grassland Administration, College of Forestry, Jiangxi Agricultural University, Nanchang 330045, China; (X.D.); (L.Z.); (H.S.); (P.W.); (S.C.); (H.L.)
| | - Hongyan Si
- East China Woody Fragrance and Flavor Engineering Research Center of National Forestry and Grassland Administration, Camphor Engineering Research Center of National Forestry and Grassland Administration, College of Forestry, Jiangxi Agricultural University, Nanchang 330045, China; (X.D.); (L.Z.); (H.S.); (P.W.); (S.C.); (H.L.)
| | - Jie Song
- Department of Natural Sciences, University of Michigan-Flint, 303E Kearsley, Flint, MI 48502, USA;
| | - Peng Wang
- East China Woody Fragrance and Flavor Engineering Research Center of National Forestry and Grassland Administration, Camphor Engineering Research Center of National Forestry and Grassland Administration, College of Forestry, Jiangxi Agricultural University, Nanchang 330045, China; (X.D.); (L.Z.); (H.S.); (P.W.); (S.C.); (H.L.)
| | - Shangxing Chen
- East China Woody Fragrance and Flavor Engineering Research Center of National Forestry and Grassland Administration, Camphor Engineering Research Center of National Forestry and Grassland Administration, College of Forestry, Jiangxi Agricultural University, Nanchang 330045, China; (X.D.); (L.Z.); (H.S.); (P.W.); (S.C.); (H.L.)
| | - Hai Luo
- East China Woody Fragrance and Flavor Engineering Research Center of National Forestry and Grassland Administration, Camphor Engineering Research Center of National Forestry and Grassland Administration, College of Forestry, Jiangxi Agricultural University, Nanchang 330045, China; (X.D.); (L.Z.); (H.S.); (P.W.); (S.C.); (H.L.)
| | - Xiaoping Rao
- College of Chemical Engineering, Huaqiao University, Xiamen 361021, China;
| | - Zongde Wang
- East China Woody Fragrance and Flavor Engineering Research Center of National Forestry and Grassland Administration, Camphor Engineering Research Center of National Forestry and Grassland Administration, College of Forestry, Jiangxi Agricultural University, Nanchang 330045, China; (X.D.); (L.Z.); (H.S.); (P.W.); (S.C.); (H.L.)
- Correspondence: (Z.W.); (S.L.); Tel.: +86-0791-83813243 (S.L.)
| | - Shengliang Liao
- East China Woody Fragrance and Flavor Engineering Research Center of National Forestry and Grassland Administration, Camphor Engineering Research Center of National Forestry and Grassland Administration, College of Forestry, Jiangxi Agricultural University, Nanchang 330045, China; (X.D.); (L.Z.); (H.S.); (P.W.); (S.C.); (H.L.)
- Correspondence: (Z.W.); (S.L.); Tel.: +86-0791-83813243 (S.L.)
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28
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Li Q, Kang C. Structures and Dynamics of Dengue Virus Nonstructural Membrane Proteins. MEMBRANES 2022; 12:membranes12020231. [PMID: 35207152 PMCID: PMC8880049 DOI: 10.3390/membranes12020231] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 02/11/2022] [Accepted: 02/15/2022] [Indexed: 02/01/2023]
Abstract
Dengue virus is an important human pathogen threating people, especially in tropical and sub-tropical regions. The viral genome has one open reading frame and encodes one polyprotein which can be processed into structural and nonstructural (NS) proteins. Four of the seven nonstructural proteins, NS2A, NS2B, NS4A and NS4B, are membrane proteins. Unlike NS3 or NS5, these proteins do not harbor any enzymatic activities, but they play important roles in viral replication through interactions with viral or host proteins to regulate important pathways and enzymatic activities. The location of these proteins on the cell membrane and the functional roles in viral replication make them important targets for antiviral development. Indeed, NS4B inhibitors exhibit antiviral activities in different assays. Structural studies of these proteins are hindered due to challenges in crystallization and the dynamic nature of these proteins. In this review, the function and membrane topologies of dengue nonstructural membrane proteins are presented. The roles of solution NMR spectroscopy in elucidating the structure and dynamics of these proteins are introduced. The success in the development of NS4B inhibitors proves that this class of proteins is an attractive target for antiviral development.
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Affiliation(s)
- Qingxin Li
- Guangdong Provincial Engineering Laboratory of Biomass High Value Utilization, Institute of Biological and Medical Engineering, Guangdong Academy of Sciences, Guangzhou 510316, China
- Correspondence: (Q.L.); (C.K.)
| | - Congbao Kang
- Experimental Drug Development Centre, Agency for Science, Technology and Research, 10 Biopolis Road, #5-01, Singapore 138670, Singapore
- Correspondence: (Q.L.); (C.K.)
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Dell'Avalle C, D'Amico F, Gabbiadini R, Dal Buono A, Pugliese N, Zilli A, Furfaro F, Fiorino G, Allocca M, Peyrin-Biroulet L, Danese S. JAK inhibitors in crohn's disease: ready to go? Expert Opin Investig Drugs 2022; 31:145-161. [PMID: 35164629 DOI: 10.1080/13543784.2022.2032639] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION Crohn's disease (CD) is a chronic, relapsing inflammatory bowel disease that can lead to significant organ damage and impaired quality of life. To date, a considerable proportion of patients does not respond to biologic compounds. It is, therefore, necessary to find alternative options with adequate efficacy and safety profiles in order to increase the chances of obtaining an enduring remission of disease. Janus kinase (JAK) inhibitors are a new class of compounds that might well serve this purpose. The aim of our review is to report the available data from clinical trials testing these new drugs in patients suffering from CD. AREAS COVERED PubMed database and ClinicalTrials.gov website were consulted in order to find the clinical trials evaluating the efficacy and safety profiles of JAK-inhibitors in CD patients, including the following compounds: tofacitinib, filgotinib, upadacitinib, TD-1473, and Pf-06651600/Pf-06700841. EXPERT OPINION JAK-inhibitors are a promising class of oral compounds in moderate-severe CD. Further clinical trials are necessary in order to implement the available knowledge, especially on their long-term safety issues.
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Affiliation(s)
| | - Ferdinando D'Amico
- Department of Biomedical Sciences, Humanitas University, Milan, Italy.,Department of Gastroenterology and Endoscopy, IRCCS Ospedale San Raffaele and Vita-Salute San Raffaele University, Milan, Italy
| | | | - Arianna Dal Buono
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Nicola Pugliese
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Alessandra Zilli
- Department of Gastroenterology and Endoscopy, IRCCS Ospedale San Raffaele and Vita-Salute San Raffaele University, Milan, Italy
| | | | - Gionata Fiorino
- Department of Gastroenterology and Endoscopy, IRCCS Ospedale San Raffaele and Vita-Salute San Raffaele University, Milan, Italy
| | - Mariangela Allocca
- Department of Gastroenterology and Endoscopy, IRCCS Ospedale San Raffaele and Vita-Salute San Raffaele University, Milan, Italy
| | - Laurent Peyrin-Biroulet
- Department of Gastroenterology and Inserm Ngere U1256, University Hospital of Nancy, University of Lorraine, France
| | - Silvio Danese
- Department of Gastroenterology and Endoscopy, IRCCS Ospedale San Raffaele and Vita-Salute San Raffaele University, Milan, Italy
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30
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Conformations and stability of capsaicin in bulk solvents: A molecular dynamics study. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.117794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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31
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Nigro E, Daniele A, Salzillo A, Ragone A, Naviglio S, Sapio L. AdipoRon and Other Adiponectin Receptor Agonists as Potential Candidates in Cancer Treatments. Int J Mol Sci 2021; 22:ijms22115569. [PMID: 34070338 PMCID: PMC8197554 DOI: 10.3390/ijms22115569] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/20/2021] [Accepted: 05/23/2021] [Indexed: 12/18/2022] Open
Abstract
The high mortality rate together with an ever-growing number of annual cases have defined neoplastic disorders as “the real 21st-century disease”. Its dubious distinction also results from conventional therapy failure, which has made cancer an orphan disease. Therefore, innovative and alternative therapeutic strategies are mandatory. The ability to leverage human naturally occurring anti-tumor defenses has always represented a fascinating perspective, and the immuno blockage approval in cancer treatment represents in timeline the latest success. As a multifunctional organ, adipose tissue releases a large amount of adipokines having both carcinogenic and antitumor properties. The negative correlation between serum levels and risk for developing malignancies, as well as the huge number of existing preclinical studies, have identified adiponectin as a potential anticancer adipokine. Nevertheless, its usage in clinical has constantly clashed with the inability to reproduce a mimic synthetic compound. Between 2011 and 2013, two distinct adiponectin receptor agonists were recognized, opening new scenarios even in cancer. Here, we review the first orally active adiponectin receptor agonists AdipoRon, from the discovery to the anticancer evidence. Including our latest findings in osteosarcoma models, we summarize AdipoRon and other existing agonists state-of-art, questioning about the feasibility assessment of this strategy in cancer treatment.
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Affiliation(s)
- Ersilia Nigro
- Dipartimento di Scienze e Tecnologie Ambientali Biologiche Farmaceutiche, Università degli Studi della Campania “Luigi Vanvitelli”, 81100 Caserta, Italy; (E.N.); (A.D.)
- CEINGE-Biotecnologie Avanzate Scarl, 80145 Napoli, Italy
| | - Aurora Daniele
- Dipartimento di Scienze e Tecnologie Ambientali Biologiche Farmaceutiche, Università degli Studi della Campania “Luigi Vanvitelli”, 81100 Caserta, Italy; (E.N.); (A.D.)
- CEINGE-Biotecnologie Avanzate Scarl, 80145 Napoli, Italy
| | - Alessia Salzillo
- Dipartimento di Medicina di Precisione, Università degli Studi della Campania “Luigi Vanvitelli”, 80138 Napoli, Italy; (A.S.); (A.R.); (L.S.)
| | - Angela Ragone
- Dipartimento di Medicina di Precisione, Università degli Studi della Campania “Luigi Vanvitelli”, 80138 Napoli, Italy; (A.S.); (A.R.); (L.S.)
| | - Silvio Naviglio
- Dipartimento di Medicina di Precisione, Università degli Studi della Campania “Luigi Vanvitelli”, 80138 Napoli, Italy; (A.S.); (A.R.); (L.S.)
- Correspondence:
| | - Luigi Sapio
- Dipartimento di Medicina di Precisione, Università degli Studi della Campania “Luigi Vanvitelli”, 80138 Napoli, Italy; (A.S.); (A.R.); (L.S.)
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Discovery and Design of Novel Small Molecule GSK-3 Inhibitors Targeting the Substrate Binding Site. Int J Mol Sci 2020; 21:ijms21228709. [PMID: 33218072 PMCID: PMC7698860 DOI: 10.3390/ijms21228709] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/15/2020] [Accepted: 11/17/2020] [Indexed: 02/07/2023] Open
Abstract
The serine/threonine kinase, GSK-3, is a promising drug discovery target for treating multiple pathological disorders. Most GSK-3 inhibitors that were developed function as ATP competitive inhibitors, with typical limitations in specificity, safety and drug-induced resistance. In contrast, substrate competitive inhibitors (SCIs), are considered highly selective, and more suitable for clinical practice. The development of SCIs has been largely neglected in the past because the ambiguous, undefined nature of the substrate-binding site makes them difficult to design. In this study, we used our previously described structural models of GSK-3 bound to SCI peptides, to design a pharmacophore model and to virtually screen the “drug-like” Zinc database (~6.3 million compounds). We identified leading hits that interact with critical binding elements in the GSK-3 substrate binding site and are chemically distinct from known GSK-3 inhibitors. Accordingly, novel GSK-3 SCI compounds were designed and synthesized with IC50 values of~1–4 μM. Biological activity of the SCI compound was confirmed in cells and in primary neurons that showed increased β-catenin levels and reduced tau phosphorylation in response to compound treatment. We have generated a new type of small molecule GSK-3 inhibitors and propose to use this strategy to further develop SCIs for other protein kinases.
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