1
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Faizan S, Wali AF, Talath S, Rehman MU, Sivamani Y, Nilugal KC, Shivangere NB, Attia SM, Nadeem A, Elayaperumal S, Kumar BRP. Novel dihydropyrimidines as promising EGFR & HER2 inhibitors: Insights from experimental and computational studies. Eur J Med Chem 2024; 275:116607. [PMID: 38908102 DOI: 10.1016/j.ejmech.2024.116607] [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: 04/27/2024] [Revised: 06/10/2024] [Accepted: 06/14/2024] [Indexed: 06/24/2024]
Abstract
Dihydropyrimidines are widely recognized for their diverse biological properties and are often synthesized by the Biginelli reactions. In this backdrop, a novel series of Biginelli dihydropyrimidines were designed, synthesized, purified, and analyzed by FT-IR, 1H NMR, 13C NMR, and mass spectrometry. Anticancer activity against MCF-7 breast cancer cells was evaluated as part of their cytotoxicity in comparison with the normal Vero cells. The cytotoxicity of dihydropyrimidines ranges from moderate to significant. Among the 38 dihydropyrimidines screened, compounds 16, 21, and 39 exhibited significant cytotoxicity. These 3 compounds were subjected to flow cytometry studies and EGFRwt Kinase inhibition assay using lapatinib as a standard. The study included evaluation for the inhibition of EGFR and HER2 expression at five different concentrations. At a concentration of 1000 nM compound 21 showed 98.51 % and 96.79 % inhibition of EGFR and HER2 expression. Moreover, compounds 16, 21 and 39 significantly inhibited EGFRwt activity with IC50 = 69.83, 37.21 and 76.79 nM, respectively. In addition, 3D-QSAR experiments were conducted to elucidate Structure activity relationships in a 3D grid space by comparing the experimental and predicted cytotoxic activities. Molecular docking studies were performed to validate the results by in silico method. All together, we developed a new series of Biginelli dihydropyrimidines as dual EGFR/HER2 inhibitors.
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Affiliation(s)
- Syed Faizan
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, Mysuru 570015, Constituent College of the JSS Academy of Higher Education & Research, Mysuru, 570015, India
| | - Adil Farooq Wali
- Department of Pharmaceutical Chemistry, RAK College of Pharmacy, RAK Medical & Health Sciences University, Ras Al Khaimah, United Arab Emirates
| | - Sirajunisa Talath
- Department of Pharmaceutical Chemistry, RAK College of Pharmacy, RAK Medical & Health Sciences University, Ras Al Khaimah, United Arab Emirates
| | - Muneeb U Rehman
- Department of Clinical Pharmacy, College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Yuvaraj Sivamani
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, Mysuru 570015, Constituent College of the JSS Academy of Higher Education & Research, Mysuru, 570015, India
| | - Kiran C Nilugal
- School of Pharmacy, Management and Science University, Selangor, 40100, Malaysia
| | | | - Sabry M Attia
- Department of Pharmacology & Toxicology, College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Ahmed Nadeem
- Department of Pharmacology & Toxicology, College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Sumitha Elayaperumal
- Department of Biotechnology and Bioinformatics, JSS Academy of Higher Education and Research, Mysore, Karnataka, India
| | - B R Prashantha Kumar
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, Mysuru 570015, Constituent College of the JSS Academy of Higher Education & Research, Mysuru, 570015, India.
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2
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Chinnadurai RK, Ponne S, Chitra L, Kumar R, Thayumanavan P, Subramanian B. Pharmacoinformatic approach to identify potential phytochemicals against SARS-CoV-2 spike receptor-binding domain in native and variants of concern. Mol Divers 2023; 27:2741-2766. [PMID: 36547813 PMCID: PMC9773690 DOI: 10.1007/s11030-022-10580-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 11/24/2022] [Indexed: 12/24/2022]
Abstract
Severe acute respiratory syndrome-related coronavirus-2 (SARS-CoV-2) pathogenesis is initiated by the binding of SARS-CoV-2 spike (S) protein with the angiotensin-converting enzyme 2 receptor (ACE2R) on the host cell surface. The receptor-binding domain (RBD) of the S protein mediates the binding and is more prone to mutations resulting in the generation of different variants. Recently, molecules with the potential to inhibit the interaction of S protein with ACE2R have been of interest due to their therapeutic value. In this context, the present work was performed to identify potential RBD binders from the Indian medicinal plant's phytochemical database through virtual screening, molecular docking, and molecular dynamic simulation. Briefly, 1578 compounds filtered from 9596 phytochemicals were chosen for screening against the RBD of the native SARS-CoV-2 S protein. Based on the binding energy, the top 30 compounds were selected and re-docked individually against the native and five variants of concern (VOCs: alpha, beta, gamma, delta, and omicron) of SARS-CoV-2. Four phytochemicals, namely withanolide F, serotobenine, orobanchol, and gibberellin A51, were found to be potential RBD binders in native and all SARS-CoV-2 VOCs. Among the four, withanolide F exhibited lower binding energy (- 10.84 to - 8.56 kcal/mol) and better ligand efficiency (- 0.3 to - 0.25) against all forms of RBD and hence was subjected to a 100 ns MD simulation which confirmed its stringent binding to the RBDs in native and VOCs. The study prioritizes withanolide F as a prospective COVID-19 (Coronavirus disease) therapeutic agent based on the observations. It warrants deeper investigations into the four promising leads for understanding their precise therapeutic value.
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Affiliation(s)
- Raj Kumar Chinnadurai
- Mahatma Gandhi Medical Advanced Research Institute, Sri Balaji Vidhyapeeth (Deemed to be University), Pondicherry, 607402, India.
| | - Saravanaraman Ponne
- Department of Biotechnology, Pondicherry University, Pondicherry, 605014, India
| | - Loganathan Chitra
- Department of Biochemistry, Periyar University, Salem, Tamil Nadu, 636011, India
| | - Rajender Kumar
- Division of Glycoscience, Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, AlbaNova University Center, 106 91, Stockholm, Sweden
| | | | - Balanehru Subramanian
- School of Biological Sciences, Sri Balaji Vidhyapeeth (Deemed to be University), Pondicherry, 607402, India
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3
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Wang S, Zhang Y, Liang C, Zhang Y, Zhan R, Huang H. Skeletal Editing of Chromone-Fused Dienes to Cyclopropane by Photochemical Carbon Deletion. Org Lett 2023; 25:8269-8273. [PMID: 37955863 DOI: 10.1021/acs.orglett.3c03317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2023]
Abstract
A visible-light-driven, photocatalyst-free, air-assisted carbon cleavage of dienes was achieved. Photochemical editing of dienes via an electron donor-acceptor (EDA) complex facilitates direct access to cyclopropane derivatives. This innovative methodology creates an opportunity for the efficient access to valuable cyclopropane derivatives under mild and ambient conditions.
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Affiliation(s)
- Shuzhong Wang
- Key Laboratory of Chinese Medicinal Resource from Lingnan, Ministry of Education, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, People's Republic of China
| | - Yili Zhang
- Key Laboratory of Chinese Medicinal Resource from Lingnan, Ministry of Education, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, People's Republic of China
| | - Chuyun Liang
- Key Laboratory of Chinese Medicinal Resource from Lingnan, Ministry of Education, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, People's Republic of China
| | - Yue Zhang
- Key Laboratory of Chinese Medicinal Resource from Lingnan, Ministry of Education, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, People's Republic of China
| | - Ruoting Zhan
- Key Laboratory of Chinese Medicinal Resource from Lingnan, Ministry of Education, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, People's Republic of China
| | - Huicai Huang
- Key Laboratory of Chinese Medicinal Resource from Lingnan, Ministry of Education, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, People's Republic of China
- Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, Shenzhen 518055, People's Republic of China
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4
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Bak A, Kozik V, Swietlicka A, Baran W, Smolinski A, Zięba A. Towards Symmetric Thioamides: Microwave-Aided Synthesis of Terephthalic Acid Derivatives. Pharmaceuticals (Basel) 2023; 16:984. [PMID: 37513896 PMCID: PMC10385826 DOI: 10.3390/ph16070984] [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: 06/24/2023] [Revised: 07/05/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2023] Open
Abstract
The multistep synthesis of novel bis-terephthalthioamides based on methyl esters of amino acids (AAs) was proposed using conventional heating and microwave-assisted approaches. In fact, the comparative case study on the thionation of new symmetrical diamides with Lawesson's reagent (LR) was performed. The microwave-accelerated small-scale methodology was successfully employed on the whole pathway from substrates (Gly, Ala, Val, Tyr, Ser) to products (symmetrical dithioamides of terephthalic acid), resulting in significantly reduced reaction time, energy requirements, and slightly increased reaction yields when compared to conventional heating. Moreover, the intermolecular similarity of novel terephthalic acid derivatives was estimated in the multidimensional space (mDS) of the structure/property-related in silico descriptors using principal component analysis (PCA) and hierarchical clustering analysis (HCA). The distance-oriented structure/property distribution was also correlated with the experimental lipophilic data.
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Affiliation(s)
- Andrzej Bak
- Institute of Chemistry, University of Silesia, Szkolna 9, 40-006 Katowice, Poland
| | - Violetta Kozik
- Institute of Chemistry, University of Silesia, Szkolna 9, 40-006 Katowice, Poland
| | | | - Wojciech Baran
- Department of General and Analytical Chemistry, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia in Katowice, Jagiellońska 4, 41-200 Sosnowiec, Poland
| | - Adam Smolinski
- Central Mining Institute, Plac Gwarków 1, 40-166 Katowice, Poland
| | - Andrzej Zięba
- Department of Organic Chemistry, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia in Katowice, Jagiellońska 4, 41-200 Sosnowiec, Poland
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5
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Young RJ. Today's drug discovery and the shadow of the rule of 5. Expert Opin Drug Discov 2023; 18:965-972. [PMID: 37378429 DOI: 10.1080/17460441.2023.2228199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 06/19/2023] [Indexed: 06/29/2023]
Abstract
INTRODUCTION The rule of 5 developed by Lipinski et al., a landmark and prescient piece of scholarship, focused the minds of drug hunters by systematically characterizing the physical make-up of drug molecules for the first time, noting many sub-optimal compounds identified by high-throughput screening practices. Its profound influence on thinking and practices, whilst providing benefit, perhaps etched the guidelines too strongly in the minds of some drug hunters who applied the bounds too literally without understanding the implications of the underlying statistics. AREAS COVERED This opinion is based on recent key developments that take thinking, measurements, and standards beyond those first set out, particularly the influences of molecular weight and the understanding, measurement, and calculation of lipophilicity. EXPERT OPINION Techniques and technologies for physicochemical estimations set new standards. It is timely to celebrate the significance and influence of the rule of 5, whilst taking thinking to new levels with better characterizations. The shadow of the rule of 5 may be long, but it is not dark, as new measurements, predictions and principles emerge as guiding lights in the design and prioritization of higher-quality molecules redefining the meaning of beyond the rule of 5.
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Affiliation(s)
- Robert J Young
- Blue Burgundy (Drug Discovery Consultancy) Ltd, Bedford, UK
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6
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Sudaki H, Fujimoto K, Wada K, Sugano K. Phosphate buffer interferes dissolution of prazosin hydrochloride in compendial dissolution testing. Drug Metab Pharmacokinet 2023; 51:100519. [PMID: 37393739 DOI: 10.1016/j.dmpk.2023.100519] [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: 01/13/2023] [Revised: 05/27/2023] [Accepted: 06/08/2023] [Indexed: 07/04/2023]
Abstract
The purpose of this study was to elucidate the lack of supersaturation behavior in the dissolution profile of prazosin hydrochloride (PRZ-HCl) in the compendial dissolution test. The equilibrium solubility was measured by a shake-flask method. Dissolution tests were performed by a compendial paddle method with a phosphate buffer solution (pH 6.8, 50 mM phosphate). The solid form of the residual particles was identified by Raman spectroscopy. In the pH range below 6.5, the equilibrium solubility in phosphate buffer was lower than that in the unbuffered solutions (pH adjusted by HCl and NaOH). Raman spectra showed that the residual solid was a phosphate salt of PRZ. In the pH range above 6.5, the pH-solubility profiles in the phosphate buffer solutions and the unbuffered solutions were the same. The residual solid was a PRZ freebase (PRZ-FB). In the dissolution test, PRZ-HCl particles first changed to a phosphate salt within 5 min, then gradually changed to PRZ-FB after several hours. Since the intestinal fluid is buffered by the bicarbonate system in vivo, the dissolution behavior in vivo may not be properly evaluated using a phosphate buffer solution. For drugs with a low phosphate solubility product, it is necessary to consider this aspect.
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Affiliation(s)
- Hiroshi Sudaki
- Nippon Boehringer Ingelheim Co. Ltd., 6-7-5 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan.
| | - Katsuyoshi Fujimoto
- Nippon Boehringer Ingelheim Co. Ltd., 6-7-5 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan
| | - Koichi Wada
- Nippon Boehringer Ingelheim Co. Ltd., 6-7-5 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan
| | - Kiyohiko Sugano
- College of Pharmaceutical Sciences, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu, Shiga, 525-8577, Japan
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7
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Soares JX, Afonso I, Omerbasic A, Loureiro DRP, Pinto MMM, Afonso CMM. The Chemical Space of Marine Antibacterials: Diphenyl Ethers, Benzophenones, Xanthones, and Anthraquinones. Molecules 2023; 28:molecules28104073. [PMID: 37241815 DOI: 10.3390/molecules28104073] [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: 03/31/2023] [Revised: 04/28/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023] Open
Abstract
The emergence of multiresistant bacteria and the shortage of antibacterials in the drug pipeline creates the need to search for novel agents. Evolution drives the optimization of the structure of marine natural products to act as antibacterial agents. Polyketides are a vast and structurally diverse family of compounds that have been isolated from different marine microorganisms. Within the different polyketides, benzophenones, diphenyl ethers, anthraquinones, and xanthones have shown promising antibacterial activity. In this work, a dataset of 246 marine polyketides has been identified. In order to characterize the chemical space occupied by these marine polyketides, molecular descriptors and fingerprints were calculated. Molecular descriptors were analyzed according to the scaffold, and principal component analysis was performed to identify the relationships among the different descriptors. Generally, the identified marine polyketides are unsaturated, water-insoluble compounds. Among the different polyketides, diphenyl ethers tend to be more lipophilic and non-polar than the remaining classes. Molecular fingerprints were used to group the polyketides according to their molecular similarity into clusters. A total of 76 clusters were obtained, with a loose threshold for the Butina clustering algorithm, highlighting the large structural diversity of the marine polyketides. The large structural diversity was also evidenced by the visualization trees map assembled using the tree map (TMAP) unsupervised machine-learning method. The available antibacterial activity data were examined in terms of bacterial strains, and the activity data were used to rank the compounds according to their antibacterial potential. This potential ranking was used to identify the most promising compounds (four compounds) which can inspire the development of new structural analogs with better potency and absorption, distribution, metabolism, excretion, and toxicity (ADMET) properties.
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Affiliation(s)
- José X Soares
- Laboratory of Organic and Pharmaceutical Chemistry, Department of Chemical Sciences, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
- Interdisciplinary Center of Marine and Environmental Investigation (CIIMAR/CIMAR), Edifício do Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4050-208 Matosinhos, Portugal
- LAQV-REQUIMTE, Department of Chemical Sciences, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
| | - Inês Afonso
- Laboratory of Organic and Pharmaceutical Chemistry, Department of Chemical Sciences, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
| | - Adaleta Omerbasic
- Laboratory of Organic and Pharmaceutical Chemistry, Department of Chemical Sciences, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
| | - Daniela R P Loureiro
- Laboratory of Organic and Pharmaceutical Chemistry, Department of Chemical Sciences, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
- Interdisciplinary Center of Marine and Environmental Investigation (CIIMAR/CIMAR), Edifício do Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4050-208 Matosinhos, Portugal
- LAQV-REQUIMTE, Department of Chemical Sciences, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
| | - Madalena M M Pinto
- Laboratory of Organic and Pharmaceutical Chemistry, Department of Chemical Sciences, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
- Interdisciplinary Center of Marine and Environmental Investigation (CIIMAR/CIMAR), Edifício do Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4050-208 Matosinhos, Portugal
| | - Carlos M M Afonso
- Laboratory of Organic and Pharmaceutical Chemistry, Department of Chemical Sciences, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
- Interdisciplinary Center of Marine and Environmental Investigation (CIIMAR/CIMAR), Edifício do Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4050-208 Matosinhos, Portugal
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8
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Pognan F, Beilmann M, Boonen HCM, Czich A, Dear G, Hewitt P, Mow T, Oinonen T, Roth A, Steger-Hartmann T, Valentin JP, Van Goethem F, Weaver RJ, Newham P. The evolving role of investigative toxicology in the pharmaceutical industry. Nat Rev Drug Discov 2023; 22:317-335. [PMID: 36781957 PMCID: PMC9924869 DOI: 10.1038/s41573-022-00633-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/16/2022] [Indexed: 02/15/2023]
Abstract
For decades, preclinical toxicology was essentially a descriptive discipline in which treatment-related effects were carefully reported and used as a basis to calculate safety margins for drug candidates. In recent years, however, technological advances have increasingly enabled researchers to gain insights into toxicity mechanisms, supporting greater understanding of species relevance and translatability to humans, prediction of safety events, mitigation of side effects and development of safety biomarkers. Consequently, investigative (or mechanistic) toxicology has been gaining momentum and is now a key capability in the pharmaceutical industry. Here, we provide an overview of the current status of the field using case studies and discuss the potential impact of ongoing technological developments, based on a survey of investigative toxicologists from 14 European-based medium-sized to large pharmaceutical companies.
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Affiliation(s)
- Francois Pognan
- Discovery and Investigative Safety, Novartis Pharma AG, Basel, Switzerland.
| | - Mario Beilmann
- Nonclinical Drug Safety Germany, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Harrie C M Boonen
- Drug Safety, Dept of Exploratory Toxicology, Lundbeck A/S, Valby, Denmark
| | | | - Gordon Dear
- In Vitro In Vivo Translation, GlaxoSmithKline David Jack Centre for Research, Ware, UK
| | - Philip Hewitt
- Chemical and Preclinical Safety, Merck Healthcare KGaA, Darmstadt, Germany
| | - Tomas Mow
- Safety Pharmacology and Early Toxicology, Novo Nordisk A/S, Maaloev, Denmark
| | - Teija Oinonen
- Preclinical Safety, Orion Corporation, Espoo, Finland
| | - Adrian Roth
- Pharmaceutical Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | | | | | - Freddy Van Goethem
- Predictive, Investigative & Translational Toxicology, Nonclinical Safety, Janssen Research & Development, Beerse, Belgium
| | - Richard J Weaver
- Innovation Life Cycle Management, Institut de Recherches Internationales Servier, Suresnes, France
| | - Peter Newham
- Clinical Pharmacology and Safety Sciences, AstraZeneca R&D, Cambridge, UK.
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9
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Revillo Imbernon J, Chiesa L, Kellenberger E. Mining the Protein Data Bank to inspire fragment library design. Front Chem 2023; 11:1089714. [PMID: 36846858 PMCID: PMC9950109 DOI: 10.3389/fchem.2023.1089714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 01/27/2023] [Indexed: 02/12/2023] Open
Abstract
The fragment approach has emerged as a method of choice for drug design, as it allows difficult therapeutic targets to be addressed. Success lies in the choice of the screened chemical library and the biophysical screening method, and also in the quality of the selected fragment and structural information used to develop a drug-like ligand. It has recently been proposed that promiscuous compounds, i.e., those that bind to several proteins, present an advantage for the fragment approach because they are likely to give frequent hits in screening. In this study, we searched the Protein Data Bank for fragments with multiple binding modes and targeting different sites. We identified 203 fragments represented by 90 scaffolds, some of which are not or hardly present in commercial fragment libraries. By contrast to other available fragment libraries, the studied set is enriched in fragments with a marked three-dimensional character (download at 10.5281/zenodo.7554649).
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Affiliation(s)
- Julia Revillo Imbernon
- Laboratoire d’Innovation Thérapeutique, Faculté de Pharmacie, UMR7200 CNRS Université de Strasbourg, Illkirch-Graffenstaden, France
| | - Luca Chiesa
- Laboratoire d’Innovation Thérapeutique, Faculté de Pharmacie, UMR7200 CNRS Université de Strasbourg, Illkirch-Graffenstaden, France
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10
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Young RJ, Flitsch SL, Grigalunas M, Leeson PD, Quinn RJ, Turner NJ, Waldmann H. The Time and Place for Nature in Drug Discovery. JACS AU 2022; 2:2400-2416. [PMID: 36465532 PMCID: PMC9709949 DOI: 10.1021/jacsau.2c00415] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 10/06/2022] [Accepted: 10/06/2022] [Indexed: 05/31/2023]
Abstract
The case for a renewed focus on Nature in drug discovery is reviewed; not in terms of natural product screening, but how and why biomimetic molecules, especially those produced by natural processes, should deliver in the age of artificial intelligence and screening of vast collections both in vitro and in silico. The declining natural product-likeness of licensed drugs and the consequent physicochemical implications of this trend in the context of current practices are noted. To arrest these trends, the logic of seeking new bioactive agents with enhanced natural mimicry is considered; notably that molecules constructed by proteins (enzymes) are more likely to interact with other proteins (e.g., targets and transporters), a notion validated by natural products. Nature's finite number of building blocks and their interactions necessarily reduce potential numbers of structures, yet these enable expansion of chemical space with their inherent diversity of physical characteristics, pertinent to property-based design. The feasible variations on natural motifs are considered and expanded to encompass pseudo-natural products, leading to the further logical step of harnessing bioprocessing routes to access them. Together, these offer opportunities for enhancing natural mimicry, thereby bringing innovation to drug synthesis exploiting the characteristics of natural recognition processes. The potential for computational guidance to help identifying binding commonalities in the route map is a logical opportunity to enable the design of tailored molecules, with a focus on "organic/biological" rather than purely "synthetic" structures. The design and synthesis of prototype structures should pay dividends in the disposition and efficacy of the molecules, while inherently enabling greener and more sustainable manufacturing techniques.
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Affiliation(s)
| | - Sabine L. Flitsch
- Department
of Chemistry, University of Manchester,
Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Michael Grigalunas
- Department
of Chemical Biology, Max-Planck-Institute
of Molecular Physiology, Otto-Hahn Strasse 11, 44227 Dortmund, Germany
| | - Paul D. Leeson
- Paul
Leeson Consulting Limited, The Malt House, Main Street, Congerstone, Nuneaton, Warwickshire CV13 6LZ, U.K.
| | - Ronald J. Quinn
- Griffith
Institute for Drug Discovery, Griffith University, Nathan, Queensland 4111, Australia
| | - Nicholas J. Turner
- Department
of Chemistry, University of Manchester,
Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Herbert Waldmann
- Department
of Chemical Biology, Max-Planck-Institute
of Molecular Physiology, Otto-Hahn Strasse 11, 44227 Dortmund, Germany
- Faculty of
Chemistry and Chemical Biology, Technical
University of Dortmund, Otto-Hahn-Strasse 6, 44227 Dortmund, Germany
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11
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Gupta NK, Jayakumar S, Huang WC, Leyssen P, Neyts J, Bachurin SO, Hwu JR, Tsay SC. Bis(Benzofuran-1,3- N, N-heterocycle)s as Symmetric and Synthetic Drug Leads against Yellow Fever Virus. Int J Mol Sci 2022; 23:ijms232012675. [PMID: 36293531 PMCID: PMC9604066 DOI: 10.3390/ijms232012675] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 10/14/2022] [Accepted: 10/19/2022] [Indexed: 11/06/2022] Open
Abstract
The yellow fever virus (YFV) is an emerging RNA virus and has caused large outbreaks in Africa and Central and South America. The virus is often transmitted through infected mosquitoes and spreads from area to area because of international travel. Being an acute viral hemorrhagic disease, yellow fever can be prevented by an effective, safe, and reliable vaccine, but not be eliminated. Currently, there is no antiviral drug available for its cure. Thus, two series of novel bis(benzofuran−1,3-imidazolidin-4-one)s and bis(benzofuran−1,3-benzimidazole)s were designed and synthesized for the development of anti-YFV lead candidates. Among 23 new bis-conjugated compounds, 4 of them inhibited YFV strain 17D (Stamaril) on Huh-7 cells in the cytopathic effect reduction assays. These conjugates exhibited the most compelling efficacy and selectivity with an EC50 of <3.54 μM and SI of >15.3. The results are valuable for the development of novel antiviral drug leads against emerging diseases.
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Affiliation(s)
- Nitesh K. Gupta
- Department of Chemistry, Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, Hsinchu 300044, Taiwan
| | - Srinivasan Jayakumar
- Department of Chemistry, Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, Hsinchu 300044, Taiwan
| | - Wen-Chieh Huang
- Department of Chemistry, Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, Hsinchu 300044, Taiwan
| | - Pieter Leyssen
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Minderbroedersstraat 10, B-3000 Leuven, Belgium
| | - Johan Neyts
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Minderbroedersstraat 10, B-3000 Leuven, Belgium
| | - Sergey O. Bachurin
- The Institute of Physiologically Active Compounds, Russian Academy of Sciences, Chernogolovka 142432, Russia
| | - Jih Ru Hwu
- Department of Chemistry, Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, Hsinchu 300044, Taiwan
- Department of Chemistry, National Central University, Jhongli City 320317, Taiwan
- Correspondence: (J.R.H.); (S.-C.T.)
| | - Shwu-Chen Tsay
- Department of Chemistry, Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, Hsinchu 300044, Taiwan
- Department of Chemistry, National Central University, Jhongli City 320317, Taiwan
- Correspondence: (J.R.H.); (S.-C.T.)
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12
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Gupta A, Ahmad R, Siddiqui S, Yadav K, Srivastava A, Trivedi A, Ahmad B, Khan MA, Shrivastava AK, Singh GK. Flavonol morin targets host ACE2, IMP-α, PARP-1 and viral proteins of SARS-CoV-2, SARS-CoV and MERS-CoV critical for infection and survival: a computational analysis. J Biomol Struct Dyn 2022; 40:5515-5546. [PMID: 33526003 PMCID: PMC7869441 DOI: 10.1080/07391102.2021.1871863] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 12/30/2020] [Indexed: 12/31/2022]
Abstract
A sudden outbreak of a novel coronavirus SARS-CoV-2 in 2019 has now emerged as a pandemic threatening to efface the existence of mankind. In absence of any valid and appropriate vaccines to combat this newly evolved agent, there is need of novel resource molecules for treatment and prophylaxis. To this effect, flavonol morin which is found in fruits, vegetables and various medicinal herbs has been evaluated for its antiviral potential in the present study. PASS analysis of morin versus reference antiviral drugs baricitinib, remdesivir and hydroxychloroquine revealed that morin displayed no violations of Lipinski's rule of five and other druglikeness filters. Morin also displayed no tumorigenic, reproductive or irritant effects and exhibited good absorption and permeation through GI (clogP <5). In principal component analysis, morin appeared closest to baricitinib in 3D space. Morin displayed potent binding to spike glycoprotein, main protease 3CLPro and papain-like protease PLPro of SARS-CoV-2, SARS-CoV and MERS-CoV using molecular docking and significant binding to three viral-specific host proteins viz. human ACE2, importin-α and poly (ADP-ribose) polymerase (PARP)-1, further lending support to its antiviral efficacy. Additionally, morin displayed potent binding to pro-inflammatory cytokines IL-6, 8 and 10 also supporting its anti-inflammatory activity. MD simulation of morin with SARS-CoV-2 3CLPro and PLPro displayed strong stability at 300 K. Both complexes exhibited constant RMSDs of protein side chains and Cα atoms throughout the simulation run time. In conclusion, morin might hold considerable therapeutic potential for the treatment and management of not only COVID-19, but also SARS and MERS if studied further. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Anamika Gupta
- Department of Biochemistry, Era’s Lucknow Medical College and Hospital, Era University, Lucknow, UP, India
| | - Rumana Ahmad
- Department of Biochemistry, Era’s Lucknow Medical College and Hospital, Era University, Lucknow, UP, India
| | - Sahabjada Siddiqui
- Department of Biotechnology, Era’s Lucknow Medical College and Hospital, Era University, Lucknow, UP, India
| | - Kusum Yadav
- Department of Biochemistry, University of Lucknow, Lucknow, UP, India
| | - Aditi Srivastava
- Department of Biochemistry, Era’s Lucknow Medical College and Hospital, Era University, Lucknow, UP, India
| | - Anchal Trivedi
- Department of Biochemistry, Era’s Lucknow Medical College and Hospital, Era University, Lucknow, UP, India
| | - Bilal Ahmad
- Research Cell, Era’s Lucknow Medical College and Hospital, Era University, Lucknow, UP, India
| | | | - Amit Kumar Shrivastava
- Department of Pharmacology, Universal College of Medical Sciences & Hospital, Ranigaon, Bhairahawa, Rupandehi, Nepal
| | - Girish Kumar Singh
- Department of Orthopedics, Era’s Lucknow Medical College and Hospital, Era University, Lucknow, UP, India
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13
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Martins V, Fazal L, Oganesian A, Shah A, Stow J, Walton H, Wilsher N. A commentary on the use of pharmacoenhancers in the pharmaceutical industry and the implication for DMPK drug discovery strategies. Xenobiotica 2022; 52:786-796. [PMID: 36537234 DOI: 10.1080/00498254.2022.2130838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Paxlovid, a drug combining nirmatrelvir and ritonavir, was designed for the treatment of COVID-19 and its rapid development has led to emergency use approval by the FDA to reduce the impact of COVID-19 infection on patients.In order to overcome potentially suboptimal therapeutic exposures, nirmatrelvir is dosed in combination with ritonavir to boost the pharmacokinetics of the active product.Here we consider examples of drugs co-administered with pharmacoenhancers.Pharmacoenhancers have been adopted for multiple purposes such as ensuring therapeutic exposure of the active product, reducing formation of toxic metabolites, changing the route of administration, and increasing the cost-effectiveness of a therapy.We weigh the benefits and risks of this approach, examining the impact of technology developments on drug design and how enhanced integration between cross-discipline teams can improve the outcome of drug discovery.
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14
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Computer-Aided Design and Synthesis of (Functionalized quinazoline)–(α-substituted coumarin)–arylsulfonate Conjugates against Chikungunya Virus. Int J Mol Sci 2022; 23:ijms23147646. [PMID: 35886992 PMCID: PMC9322071 DOI: 10.3390/ijms23147646] [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: 05/31/2022] [Revised: 07/04/2022] [Accepted: 07/07/2022] [Indexed: 11/30/2022] Open
Abstract
Chikungunya virus (CHIKV) has repeatedly spread via the bite of an infected mosquito and affected more than 100 countries. The disease poses threats to public health and the economy in the infected locations. Many efforts have been devoted to identifying compounds that could inhibit CHIKV. Unfortunately, successful clinical candidates have not been found yet. Computations through the simulating recognition process were performed on complexation of the nsP3 protein of CHIKV with the structures of triply conjugated drug lead candidates. The outcomes provided the aid on rational design of functionalized quinazoline-(α-substituted coumarin)-arylsulfonate compounds to inhibit CHIKV in Vero cells. The molecular docking studies showed a void space around the β carbon atom of coumarin when a substituent was attached at the α position. The formed vacancy offered a good chance for a Michael addition to take place owing to steric and electronic effects. The best conjugate containing a quinazolinone moiety exhibited potency with EC50 = 6.46 μM, low toxicity with CC50 = 59.7 μM, and the selective index (SI) = 9.24. Furthermore, the corresponding 4-anilinoquinazoline derivative improved the anti-CHIKV potency to EC50 = 3.84 μM, CC50 = 72.3 μM, and SI = 18.8. The conjugate with 4-anilinoquinazoline exhibited stronger binding affinity towards the macro domain than that with quinazolinone via hydrophobic and hydrogen bond interactions.
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15
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Abstract
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Sulfur functional
groups are common motifs in bioactive molecules.
Sulfonamides are most prevalent but related aza-derivatives, in which
oxygen atoms are replaced by imidic nitrogens, such as sulfoximines
and sulfonimidamides, are gaining attraction. Despite this activity,
the double aza-variants of sulfonamides, termed sulfondiimidamides,
are almost completely absent from the literature. The reason for this
is poor synthetic accessibility. Although a recent synthesis has established
sulfondiimidamides as viable motifs, the length of the route and the
capricious nature of the key sulfondiimidoyl fluoride intermediates
mean that direct application to discovery chemistry is challenging.
Herein, we describe a two-step synthesis of sulfondiimidamides, exploiting
a hypervalent iodine-mediated amination as the key step. The starting
materials are organometallic reagents, an unsymmetrical sulfurdiimide,
and amines. The method allowed >40 examples to be prepared, including
derivatives of three sulfonamide-based drugs. The operational simplicity,
broad scope, and concise nature make this route attractive for discovery
chemistry applications.
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Affiliation(s)
- Ze-Xin Zhang
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - Charles Bell
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - Mingyan Ding
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - Michael C Willis
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
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16
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Anticancer and Anti-Metastatic Role of Thymoquinone: Regulation of Oncogenic Signaling Cascades by Thymoquinone. Int J Mol Sci 2022; 23:ijms23116311. [PMID: 35682990 PMCID: PMC9181073 DOI: 10.3390/ijms23116311] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 05/29/2022] [Accepted: 05/30/2022] [Indexed: 12/04/2022] Open
Abstract
Cancer is a life-threatening and multifaceted disease. Pioneering research works in the past three decades have mechanistically disentangled intertwined signaling networks which play contributory roles in carcinogenesis and metastasis. Phenomenal strides have been made in leveraging our scientific knowledge altogether to a new level of maturity. Rapidly accumulating wealth of information has underlined a myriad of transduction cascades which can be pharmaceutically exploited for cancer prevention/inhibition. Natural products serve as a treasure trove and compel interdisciplinary researchers to study the cancer chemopreventive roles of wide-ranging natural products in cell culture and preclinical studies. Experimental research related to thymoquinone has gradually gained momentum because of the extra-ordinary cancer chemopreventive multifunctionalities of thymoquinone. In this mini-review, we provide an overview of different cell signaling cascades reported to be regulated by thymoquinone for cancer chemoprevention. Essentially, thymoquinone efficacy has also been notably studied in animal models, which advocates for a rationale-based transition of thymoquinone from the pre-clinical pipeline to clinical trials.
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17
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Kaur S, Nieto NS, McDonald P, Beck JR, Honzatko RB, Roy A, Nelson SW. Discovery of small molecule inhibitors of Plasmodium falciparum apicoplast DNA polymerase. J Enzyme Inhib Med Chem 2022; 37:1320-1326. [PMID: 35514163 PMCID: PMC9090415 DOI: 10.1080/14756366.2022.2070909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
Malaria is caused by infection with protozoan parasites of the Plasmodium genus, which is part of the phylum Apicomplexa. Most organisms in this phylum contain a relic plastid called the apicoplast. The apicoplast genome is replicated by a single DNA polymerase (apPOL), which is an attractive target for anti-malarial drugs. We screened small-molecule libraries (206,504 compounds) using a fluorescence-based high-throughput DNA polymerase assay. Dose/response analysis and counter-screening identified 186 specific apPOL inhibitors. Toxicity screening against human HepaRG human cells removed 84 compounds and the remaining were subjected to parasite killing assays using chloroquine resistant P. falciparum parasites. Nine compounds were potent inhibitors of parasite growth and may serve as lead compounds in efforts to discover novel malaria drugs.
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Affiliation(s)
- Supreet Kaur
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, USA
| | - Nicholas S Nieto
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, USA
| | - Peter McDonald
- High Throughput Screening Laboratory, University of Kansas, Lawrence, KS, USA
| | - Josh R Beck
- Department of Biomedical Sciences, Iowa State University, Ames, IA, USA
| | - Richard B Honzatko
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, USA
| | - Anuradha Roy
- High Throughput Screening Laboratory, University of Kansas, Lawrence, KS, USA
| | - Scott W Nelson
- Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, USA
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18
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Jurczyk J, Woo J, Kim SF, Dherange BD, Sarpong R, Levin MD. Single-atom logic for heterocycle editing. NATURE SYNTHESIS 2022; 1:352-364. [PMID: 35935106 PMCID: PMC9355079 DOI: 10.1038/s44160-022-00052-1] [Citation(s) in RCA: 103] [Impact Index Per Article: 51.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Medicinal chemistry continues to be impacted by new synthetic methods. Particularly sought after, especially at the drug discovery stage, is the ability to enact the desired chemical transformations in a concise and chemospecific fashion. To this end, the field of organic synthesis has become captivated by the idea of 'molecular editing'-to rapidly build onto, change or prune molecules one atom at a time using transformations that are mild and selective enough to be employed at the late stages of a synthetic sequence. In this Review, the definition and categorization of a particularly promising subclass of molecular editing reactions, termed 'single-atom skeletal editing', are proposed. Although skeletal editing applies to both cyclic and acyclic compounds, this Review focuses on heterocycles, both for their centrality in medicinal chemistry and for the definitional clarity afforded by a focus on ring systems. A classification system is presented by highlighting methods (both historically important examples and recent advances) that achieve such transformations, with the goal to spark interest and inspire further development in this growing field.
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Affiliation(s)
- Justin Jurczyk
- Department of Chemistry, University of California, Berkeley, CA, USA
| | - Jisoo Woo
- Department of Chemistry, University of Chicago, Chicago, IL, USA
- These authors contributed equally: Jisoo Woo, Sojung F. Kim
| | - Sojung F. Kim
- Department of Chemistry, University of California, Berkeley, CA, USA
- These authors contributed equally: Jisoo Woo, Sojung F. Kim
| | - Balu D. Dherange
- Department of Chemistry, University of Chicago, Chicago, IL, USA
| | - Richmond Sarpong
- Department of Chemistry, University of California, Berkeley, CA, USA
- Correspondence should be addressed to Richmond Sarpong or Mark D. Levin. ;
| | - Mark D. Levin
- Department of Chemistry, University of Chicago, Chicago, IL, USA
- Correspondence should be addressed to Richmond Sarpong or Mark D. Levin. ;
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19
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Revillo Imbernon J, Jacquemard C, Bret G, Marcou G, Kellenberger E. Comprehensive analysis of commercial fragment libraries. RSC Med Chem 2022; 13:300-310. [PMID: 35434627 PMCID: PMC8942207 DOI: 10.1039/d1md00363a] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 12/22/2021] [Indexed: 12/26/2022] Open
Abstract
Screening of fragment libraries is a valuable approach to the drug discovery process. The quality of the library is one of the keys to success, and more particularly the design or choice of a library has to meet the specificities of the research program. In this study, we made an inventory of the commercial fragment libraries and we established a methodology which allows any library to be positioned in relation to the complete offer currently on the market, by addressing the following questions: does this chemical library look like another chemical library? What is the coverage of the current chemical space by this chemical library? What are the characteristic structural features of the fragments of this chemical library? We based our analysis on 2D and 3D chemical descriptors, framework class generation and the generative topographic map. We identified 59 270 scaffolds, which can be searched in a dedicated web site (https://gtmfrag.drugdesign.unistra.fr) and developed a model which accounts for fragment diversity while being easy to interpret (download at 10.5281/zenodo.5534434).
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Affiliation(s)
- Julia Revillo Imbernon
- Laboratoire d'Innovation Thérapeutique, UMR7200 CNRS Université de Strasbourg, Institut du Médicament de Strasbourg, Université de Strasbourg, Faculté de PharmacieIllkirch-GraffenstadenFrance
| | - Célien Jacquemard
- Laboratoire d'Innovation Thérapeutique, UMR7200 CNRS Université de Strasbourg, Institut du Médicament de Strasbourg, Université de Strasbourg, Faculté de PharmacieIllkirch-GraffenstadenFrance
| | - Guillaume Bret
- Laboratoire d'Innovation Thérapeutique, UMR7200 CNRS Université de Strasbourg, Institut du Médicament de Strasbourg, Université de Strasbourg, Faculté de PharmacieIllkirch-GraffenstadenFrance
| | - Gilles Marcou
- Laboratory of Chemoinformatics, UMR7177 CNRS Université de StrasbourgStrasbourgFrance
| | - Esther Kellenberger
- Laboratoire d'Innovation Thérapeutique, UMR7200 CNRS Université de Strasbourg, Institut du Médicament de Strasbourg, Université de Strasbourg, Faculté de PharmacieIllkirch-GraffenstadenFrance
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20
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Tsantili-Kakoulidou A, Demopoulos VJ. Drug-like Properties and Fraction Lipophilicity Index as a combined metric. ADMET AND DMPK 2022; 9:177-190. [PMID: 35300360 PMCID: PMC8920096 DOI: 10.5599/admet.1022] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 09/30/2021] [Indexed: 01/31/2023] Open
Abstract
Fraction Lipophicity Index (FLI) has been developed as a composite drug-like metric combining log P and log D in a weighted manner. In the present study, an extended data set confirmed the previously established drug-like FLI range 0-8 using two calculation systems for log P/log D assessment, the freeware MedChem Designer and ClogP. The dataset was split into two classes according to the percentage of fraction absorbed (%FA) - class 1 including drugs with high to medium absorption levels and class 2 including poorly absorbed drugs. The FLI and FLI-C (ClogP based FLI) drug-like range covers 92 % and 91 % of class 1 drugs, respectively. Using MlogP, a narrower drug-like FLI-M range 0-7 was established, covering 91 % of class 1 drugs. The dependence of the degree of ionization to intrinsic lipophilicity within the FLI (FLI-C, FLI-M) drug-like range as well as the inter-relation between the other Ro5 properties (Mw, HD, HA) was explored to define drug-like / non-drug-like combinations as a safer alternative to single properties for drug candidates' prioritization. In this sense, we propose a combined metric of Mw and the number of polar atoms (Mw/NO) to account for both size and polarity. Setting the value 50 as cutoff, a distinct differentiation between class 1 and class 2 drugs was obtained with Mw/NO>50 for more than 70 % of class 1 drugs, while the opposite was observed for class 2 drugs.
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Affiliation(s)
- Anna Tsantili-Kakoulidou
- Department of Pharmaceutical Chemistry, School of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis, Zografou, 157 71 Athens, Greece. E-mail:
| | - Vassilis J Demopoulos
- Department of Pharmaceutical Chemistry, School of Pharmacy, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece. E-mail:
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21
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Bolcato G, Heid E, Boström J. On the Value of Using 3D Shape and Electrostatic Similarities in Deep Generative Methods. J Chem Inf Model 2022; 62:1388-1398. [PMID: 35271260 PMCID: PMC8965872 DOI: 10.1021/acs.jcim.1c01535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Multiparameter optimization,
the heart of drug design, is still
an open challenge. Thus, improved methods for automated compound design
with multiple controlled properties are desired. Here, we present
a significant extension to our previously described fragment-based
reinforcement learning method (DeepFMPO) for the generation of novel
molecules with optimal properties. As before, the generative process
outputs optimized molecules similar to the input structures, now with
the improved feature of replacing parts of these molecules with fragments
of similar three-dimensional (3D) shape and electrostatics. We developed
and benchmarked a new python package, ESP-Sim, for the comparison
of the electrostatic potential and the molecular shape, allowing the
calculation of high-quality partial charges (e.g., RESP with B3LYP/6-31G**)
obtained using the quantum chemistry program Psi4. By performing comparisons
of 3D fragments, we can simulate 3D properties while overcoming the
notoriously difficult step of accurately describing bioactive conformations.
The new improved generative (DeepFMPO v3D) method is demonstrated
with a scaffold-hopping exercise identifying CDK2 bioisosteres. The
code is open-source and freely available.
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Affiliation(s)
- Giovanni Bolcato
- Molecular Modeling Section, University of Padova, 35131 Padova, Italy
| | - Esther Heid
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, 02139 Massachusetts, United States
| | - Jonas Boström
- Medicinal Chemistry, Early CVRM, BioPharmaceuticals R&D, AstraZeneca, 431 50 Mölndal, Sweden
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22
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Pitsillou E, Liang JJ, Beh RC, Prestedge J, Catak S, Hung A, Karagiannis TC. Identification of novel bioactive compounds from Olea europaea by evaluation of chemical compounds in the OliveNet™ library: in silico bioactivity and molecular modelling, and in vitro validation of hERG activity. Comput Biol Med 2022; 142:105247. [DOI: 10.1016/j.compbiomed.2022.105247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/18/2022] [Accepted: 01/18/2022] [Indexed: 11/03/2022]
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24
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Murad HAS, Alqurashi TMA, Hussien MA. Interactions of selected cardiovascular active natural compounds with CXCR4 and CXCR7 receptors: a molecular docking, molecular dynamics, and pharmacokinetic/toxicity prediction study. BMC Complement Med Ther 2022; 22:35. [PMID: 35120520 PMCID: PMC8817505 DOI: 10.1186/s12906-021-03488-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 12/06/2021] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND The chemokine CXCL12 and its two receptors (CXCR4 and CXCR7) are involved in inflammation and hematopoietic cell trafficking. This study was designed to investigate molecular docking interactions of four popular cardiovascular-active natural compounds; curcumin, resveratrol, quercetin, and eucalyptol; with these receptors and to predict their drug-like properties. We hypothesize that these compounds can modify CXCL12/CXCR4/CXCR7 pathway offering benefits for coronary artery disease patients. METHODS Docking analyses were carried and characterized by Molecular Environment (MOE) software. Protein Data Bank ( http://www.rcsb.org/ ) has been retrieved from protein structure generation and crystal structures of CXCR4 and CXCR7 receptors (PDB code = 3ODU and 6K3F). The active sites of these receptors were evaluated and extracted from full protein and molecular docking protocol was done for compounds against them. The presented parameters included docking scores, ligand binding efficiency, and hydrogen bonding. The pharmacokinetic/toxic properties (ADME/T) were calculated using SwissADME, ProTox-II, and Pred-hERG softwares to predict drug-like properties of the compounds. The thermochemical and molecular orbital analysis, and molecular dynamics simulations were also done. RESULTS All compounds showed efficient interactions with the CXCR4 and CXCR7 receptors. The docking scores toward proteins 3ODU of CXCR4 and 6K3F of CXCR7 were - 7.71 and - 7.17 for curcumin, - 5.97 and - 6.03 for quercetin, - 5.68 and - 5.49 for trans-resveratrol, and - 4.88 and - 4.70 for (1 s,4 s)-eucalyptol respectively indicating that all compounds, except quercetin, have more interactions with CXCR4 than with CXCR7. The structurally and functionally important residues in the interactive sites of docked CXCR4-complex and CXCR7-complex were identified. The ADME analysis showed that the compounds have drug-like properties. Only (1 s,4 s)-Eucalyptol has potential weak cardiotoxicity. The results of thermochemical and molecular orbital analysis and molecular dynamics simulation validated outcomes of molecular docking study. CONCLUSIONS Curcumin showed the top binding interaction against active sites of CXCR4 and CXCR7 receptors, with the best safety profile, followed by quercetin, resveratrol, and eucalyptol. All compounds demonstrated drug-like properties. Eucalyptol has promising potential because it can be used by inhalation or skin massage. To our knowledge, this is the first attempt to find binding interactions of these natural agents with CXCR4 and CXCR7 receptors and to predict their druggability.
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Affiliation(s)
- Hussam Aly Sayed Murad
- Department of Pharmacology, Faculty of Medicine, Rabigh, King Abdulaziz University, Jeddah, 21589, Saudi Arabia.
| | | | - Mostafa Aly Hussien
- Department of Chemistry, Faculty of Science, King Abdulaziz University, Jeddah, 21589, Saudi Arabia.,Department of Chemistry, Faculty of Science, Port-Said University, Port-Said, 42521, Egypt
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25
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Cherney EC, Zhang L, Lo J, Huynh T, Wei D, Ahuja V, Quesnelle C, Schieven GL, Futran A, Locke GA, Lin Z, Monereau L, Chaudhry C, Blum J, Li S, Fereshteh M, Li-Wang B, Gangwar S, Pan C, Chong C, Zhu X, Posy SL, Sack JS, Zhang P, Ruzanov M, Harner M, Akhtar F, Schroeder GM, Vite G, Fink B. Discovery of Non-Nucleotide Small-Molecule STING Agonists via Chemotype Hybridization. J Med Chem 2022; 65:3518-3538. [PMID: 35108011 DOI: 10.1021/acs.jmedchem.1c01986] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The identification of agonists of the stimulator of interferon genes (STING) pathway has been an area of intense research due to their potential to enhance innate immune response and tumor immunogenicity in the context of immuno-oncology therapy. Initial efforts to identify STING agonists focused on the modification of 2',3'-cGAMP (1) (an endogenous STING activator ligand) and other closely related cyclic dinucleotides (CDNs). While these efforts have successfully identified novel CDNs that have progressed into the clinic, their utility is currently limited to patients with solid tumors that STING agonists can be delivered to intratumorally. Herein, we report the discovery of a unique class of non-nucleotide small-molecule STING agonists that demonstrate antitumor activity when dosed intratumorally in a syngeneic mouse model.
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Affiliation(s)
- Emily C Cherney
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Liping Zhang
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Julian Lo
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Tram Huynh
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Donna Wei
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Vijay Ahuja
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Claude Quesnelle
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Gary L Schieven
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Alan Futran
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Gregory A Locke
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Zeyu Lin
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Laura Monereau
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Charu Chaudhry
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Jordan Blum
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Sha Li
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Mark Fereshteh
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Bifang Li-Wang
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Sanjeev Gangwar
- Bristol Myers Squibb Research and Development, 700 Bay Rd, Redwood City, California 94063, United States
| | - Chin Pan
- Bristol Myers Squibb Research and Development, 700 Bay Rd, Redwood City, California 94063, United States
| | - Colin Chong
- Bristol Myers Squibb Research and Development, 700 Bay Rd, Redwood City, California 94063, United States
| | - Xiao Zhu
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Shana L Posy
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - John S Sack
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Ping Zhang
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Max Ruzanov
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Mary Harner
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Fahad Akhtar
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Gretchen M Schroeder
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Gregory Vite
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
| | - Brian Fink
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543, United States
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Hwu JR, Kapoor M, Gupta NK, Tsay SC, Huang WC, Tan KT, Hu YC, Lyssen P, Neyts J. Synthesis and antiviral activities of quinazolinamine–coumarin conjugates toward chikungunya and hepatitis C viruses. Eur J Med Chem 2022; 232:114164. [DOI: 10.1016/j.ejmech.2022.114164] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/21/2022] [Accepted: 01/26/2022] [Indexed: 11/04/2022]
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Soares JX, Loureiro DRP, Dias AL, Reis S, Pinto MMM, Afonso CMM. Bioactive Marine Xanthones: A Review. Mar Drugs 2022; 20:58. [PMID: 35049913 PMCID: PMC8778107 DOI: 10.3390/md20010058] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 12/27/2021] [Accepted: 12/29/2021] [Indexed: 02/08/2023] Open
Abstract
The marine environment is an important source of specialized metabolites with valuable biological activities. Xanthones are a relevant chemical class of specialized metabolites found in this environment due to their structural variety and their biological activities. In this work, a comprehensive literature review of marine xanthones reported up to now was performed. A large number of bioactive xanthone derivatives (169) were identified, and their structures, biological activities, and natural sources were described. To characterize the chemical space occupied by marine-derived xanthones, molecular descriptors were calculated. For the analysis of the molecular descriptors, the xanthone derivatives were grouped into five structural categories (simple, prenylated, O-heterocyclic, complex, and hydroxanthones) and six biological activities (antitumor, antibacterial, antidiabetic, antifungal, antiviral, and miscellaneous). Moreover, the natural product-likeness and the drug-likeness of marine xanthones were also assessed. Marine xanthone derivatives are rewarding bioactive compounds and constitute a promising starting point for the design of other novel bioactive molecules.
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Affiliation(s)
- José X. Soares
- Laboratório Associado para a Química Verde (LAQV), Rede de Química e Tecnologia (REQUIMTE), Department of Chemical Sciences, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal; (J.X.S.); (D.R.P.L.); (S.R.)
- Laboratory of Organic and Pharmaceutical Chemistry, Department of Chemical Sciences, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal; (A.L.D.); (M.M.M.P.)
| | - Daniela R. P. Loureiro
- Laboratório Associado para a Química Verde (LAQV), Rede de Química e Tecnologia (REQUIMTE), Department of Chemical Sciences, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal; (J.X.S.); (D.R.P.L.); (S.R.)
- Laboratory of Organic and Pharmaceutical Chemistry, Department of Chemical Sciences, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal; (A.L.D.); (M.M.M.P.)
- Interdisciplinary Center of Marine and Environmental Investigation (CIIMAR/CIMAR), Edifício do Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4050-208 Matosinhos, Portugal
| | - Ana Laura Dias
- Laboratory of Organic and Pharmaceutical Chemistry, Department of Chemical Sciences, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal; (A.L.D.); (M.M.M.P.)
| | - Salete Reis
- Laboratório Associado para a Química Verde (LAQV), Rede de Química e Tecnologia (REQUIMTE), Department of Chemical Sciences, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal; (J.X.S.); (D.R.P.L.); (S.R.)
| | - Madalena M. M. Pinto
- Laboratory of Organic and Pharmaceutical Chemistry, Department of Chemical Sciences, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal; (A.L.D.); (M.M.M.P.)
- Interdisciplinary Center of Marine and Environmental Investigation (CIIMAR/CIMAR), Edifício do Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4050-208 Matosinhos, Portugal
| | - Carlos M. M. Afonso
- Laboratory of Organic and Pharmaceutical Chemistry, Department of Chemical Sciences, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal; (A.L.D.); (M.M.M.P.)
- Interdisciplinary Center of Marine and Environmental Investigation (CIIMAR/CIMAR), Edifício do Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4050-208 Matosinhos, Portugal
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Rahal A, Sharma DK, Kumar A, Sharma N, Dayal D. In silico to In vivo development of a polyherbal against Haemonchus contortus. Heliyon 2022; 8:e08789. [PMID: 35106389 PMCID: PMC8789534 DOI: 10.1016/j.heliyon.2022.e08789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/09/2021] [Accepted: 01/13/2022] [Indexed: 10/25/2022] Open
Abstract
Haemonchus contortus is a major constraint in the development of small ruminant subsector due to significant production losses incurred by it. The present study explores the antiparasitic potential of three anthelmintic plants (Butea monosperma, Vitex negundo and Catharanthus roseus (L.) G.Don) against H. contortus taking albendazole as the standard. In silico molecular docking and pharmacokinetic prediction studies were conducted with known bioactive molecules of these plants (palasonin, vinblastine, vincristine, betulinic acid and ursolic acid) against Glutamate Dehydrogenase (GDH) and tubulin molecules of the parasite. Methanolic extracts of these herbs were fractionated (hexane, ethyl acetate, chloroform and methanol) and used in in vitro larvicidal studies. Based on the in vitro data, two herbal prototypes were developed and clinically tested. All the 5 ligand molecules showed better binding affnity for GDH and tubulin protein as compared with albendazole and shared similar binding site in the core of the GDH hexamer with slight variations. Albendazole approximately stacked against GLY190A residue, showing hydrophobic interactions with PRO157A and a Pi-cation electrostatic interaction with ARG390 along with four hydrogen bonds. Vincristine formed 2 pi-anionic electrostatic bonds with ASP158 of B and C subunits alongwith hydrogen bonding and hydrophobic interaction and an additional pi-anion electrostatic interaction at ASP158A for vinblastine. Albendazole bound to α-tubulin next to colchicine site whereas vinblastine is bound at the nearby laulimalide/peloruside site of the dimer. Betulinic acid showed lateral interaction between the H2-H3 loop of one alpha subunit and H10 of the adjacent alpha subunit of two tubulin dimers. Ursolic acid and palasonin bound at the intradimer N site of microtubulin involving the H1-H7 and H1-H2 zone, respectively. The in vitro studies demonstrated good dose dependent anthelmintic potential. Both the prototypes were quite efficacious in clearing the infection, keeping it to a minimal for more than 5 months, probably, through direct anthelmintic effect through GDH, tubulin depolymerization and uncoupling as well as indirectly through immunomodulation along with antioxidant and anti-inflammatory properties.
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Affiliation(s)
- Anu Rahal
- Division of Animal Health, ICAR-Central Institute for Research on Goats, Makhdoom, Farah, Mathura, 281122, UP, India
| | - D K Sharma
- Division of Animal Health, ICAR-Central Institute for Research on Goats, Makhdoom, Farah, Mathura, 281122, UP, India
| | - Ashok Kumar
- Division of Animal Health, ICAR-Central Institute for Research on Goats, Makhdoom, Farah, Mathura, 281122, UP, India
| | - Nitika Sharma
- Division of Animal Health, ICAR-Central Institute for Research on Goats, Makhdoom, Farah, Mathura, 281122, UP, India
| | - Deen Dayal
- Division of Animal Health, ICAR-Central Institute for Research on Goats, Makhdoom, Farah, Mathura, 281122, UP, India
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Matthee C, Terre'Blanche G, Janse van Rensburg HD, Aucamp J, Legoabe LJ. Chalcone-inspired rA 1 /A 2A adenosine receptor ligands: Ring closure as an alternative to a reactive substructure. Chem Biol Drug Des 2021; 99:416-437. [PMID: 34878728 DOI: 10.1111/cbdd.13999] [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: 09/07/2021] [Revised: 10/21/2021] [Accepted: 10/30/2021] [Indexed: 11/30/2022]
Abstract
Over the past few years, great progress has been made in the development of high-affinity adenosine A1 and/or A2A receptor antagonists-promising agents for the potential treatment of Parkinson's disease. Unfortunately, many of these compounds raise structure-related concerns. The present study investigated the effect of ring closures on the rA1 /A2A affinity of compounds containing a highly reactive α,β-unsaturated carbonyl system, hence providing insight into the potential of heterocycles to address these concerns. A total of 12 heterocyclic compounds were synthesised and evaluated in silico and in vitro. The test compounds performed well upon qualitative assessment of drug-likeness and were generally found to be free from potentially problematic fragments. Most also showed low/weak cytotoxicity. Results from radioligand binding experiments confirm that heterocycles (particularly 2-substituted 3-cyanopyridines) can replace the promiscuous α,β-unsaturated ketone functional group without compromising A1 /A2A affinity. Structure-activity relationships highlighted the importance of hydrogen bonds in binding to the receptors of interest. Compounds 3c (rA1 Ki = 16 nM; rA2A Ki = 65 nM) and 8a (rA1 Ki = 102 nM; rA2A Ki = 37 nM), which both act as A1 antagonists, showed significant dual A1 /A2A affinity and may, therefore, inspire further investigation into heterocycles as potentially safe and potent adenosine receptor antagonists.
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Affiliation(s)
- Chrisna Matthee
- Centre of Excellence for Pharmaceutical Sciences, North-West University, Potchefstroom, South Africa
| | - Gisella Terre'Blanche
- Centre of Excellence for Pharmaceutical Sciences, North-West University, Potchefstroom, South Africa.,Pharmaceutical Chemistry, School of Pharmacy, North-West University, Potchefstroom, South Africa
| | | | - Janine Aucamp
- Centre of Excellence for Pharmaceutical Sciences, North-West University, Potchefstroom, South Africa
| | - Lesetja J Legoabe
- Centre of Excellence for Pharmaceutical Sciences, North-West University, Potchefstroom, South Africa
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Empel A, Bak A, Kozik V, Latocha M, Cizek A, Jampilek J, Suwinska K, Sochanik A, Zieba A. Towards Property Profiling: SYNTHESIS and SAR Probing of New Tetracyclic Diazaphenothiazine Analogues. Int J Mol Sci 2021; 22:ijms222312826. [PMID: 34884631 PMCID: PMC8658022 DOI: 10.3390/ijms222312826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 11/22/2021] [Accepted: 11/25/2021] [Indexed: 11/16/2022] Open
Abstract
A series of new tertiary phenothiazine derivatives containing a quinoline and a pyridine fragment was synthesized by the reaction of 1-methyl-3-benzoylthio-4-butylthioquinolinium chloride with 3-aminopyridine derivatives bearing various substituents on the pyridine ring. The direction and mechanism of the cyclization reaction of intermediates with the structure of 1-methyl-4-(3-pyridyl)aminoquinolinium-3-thiolate was related to the substituents in the 2- and 4-pyridine position. The structures of the compounds were analyzed using 1H, 13C NMR (COSY, HSQC, HMBC) and X-ray analysis, respectively. Moreover, the antiproliferative activity against tumor cells (A549, T47D, SNB-19) and a normal cell line (NHDF) was tested. The antibacterial screening of all the compounds was conducted against the reference and quality control strain Staphylococcus aureus ATCC 29213, three clinical isolates of methicillin-resistant S. aureus (MRSA). In silico computation of the intermolecular similarity was performed using principal component analysis (PCA) and hierarchical clustering analysis (HCA) on the pool of structure/property-related descriptors calculated for the novel tetracyclic diazaphenothiazine derivatives. The distance-oriented property evaluation was correlated with the experimental anticancer activities and empirical lipophilicity as well. The quantitative shape-based comparison was conducted using the CoMSA method in order to indicate the potentially valid steric, electronic and lipophilic properties. Finally, the numerical sampling of similarity-related activity landscape (SALI) provided a subtle picture of the SAR trends.
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Affiliation(s)
- Anna Empel
- Department of Organic Chemistry, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia in Katowice, Jagiellońska 4, 41-200 Sosnowiec, Poland;
| | - Andrzej Bak
- Institute of Chemistry, University of Silesia, Szkolna 9, 40-007 Katowice, Poland;
- Correspondence: (A.B.); (A.Z.)
| | - Violetta Kozik
- Institute of Chemistry, University of Silesia, Szkolna 9, 40-007 Katowice, Poland;
| | - Malgorzata Latocha
- Department of Cell Biology, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia in Katowice, Jedności 9, 41-200 Sosnowiec, Poland;
| | - Alois Cizek
- Department of Infectious Diseases and Microbiology, Faculty of Veterinary Medicine, University of Veterinary Sciences Brno, Palackeho 1946/1, 61242 Brno, Czech Republic;
| | - Josef Jampilek
- Department of Analytical Chemistry, Faculty of Natural Sciences, Comenius University, Ilkovicova 6, 84215 Bratislava, Slovakia;
- Department of Chemical Biology, Faculty of Science, Palacky University Olomouc, Slechtitelu 27, 78371 Olomouc, Czech Republic
| | - Kinga Suwinska
- Faculty of Mathematics and Natural Sciences, Cardinal Stefan Wyszyński University, K. Woycickiego 1/3, 01-938 Warszawa, Poland;
| | - Aleksander Sochanik
- Center for Translational Research and Molecular Biology of Cancer, Maria Skłodowska-Curie National Research Institute of Oncology, Wybrzeże AK 15, 44-101 Gliwice, Poland;
| | - Andrzej Zieba
- Department of Organic Chemistry, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia in Katowice, Jagiellońska 4, 41-200 Sosnowiec, Poland;
- Correspondence: (A.B.); (A.Z.)
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Vijayan RSK, Kihlberg J, Cross JB, Poongavanam V. Enhancing preclinical drug discovery with artificial intelligence. Drug Discov Today 2021; 27:967-984. [PMID: 34838731 DOI: 10.1016/j.drudis.2021.11.023] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 10/15/2021] [Accepted: 11/19/2021] [Indexed: 12/14/2022]
Abstract
Artificial intelligence (AI) is becoming an integral part of drug discovery. It has the potential to deliver across the drug discovery and development value chain, starting from target identification and reaching through clinical development. In this review, we provide an overview of current AI technologies and a glimpse of how AI is reimagining preclinical drug discovery by highlighting examples where AI has made a real impact. Considering the excitement and hyperbole surrounding AI in drug discovery, we aim to present a realistic view by discussing both opportunities and challenges in adopting AI in drug discovery.
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Affiliation(s)
- R S K Vijayan
- Institute for Applied Cancer Science, MD Anderson Cancer Center, Houston, TX, USA
| | - Jan Kihlberg
- Department of Chemistry-BMC, Uppsala University, Uppsala, Sweden
| | - Jason B Cross
- Institute for Applied Cancer Science, MD Anderson Cancer Center, Houston, TX, USA.
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MRlogP: Transfer Learning Enables Accurate logP Prediction Using Small Experimental Training Datasets. Processes (Basel) 2021. [DOI: 10.3390/pr9112029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Small molecule lipophilicity is often included in generalized rules for medicinal chemistry. These rules aim to reduce time, effort, costs, and attrition rates in drug discovery, allowing the rejection or prioritization of compounds without the need for synthesis and testing. The availability of high quality, abundant training data for machine learning methods can be a major limiting factor in building effective property predictors. We utilize transfer learning techniques to get around this problem, first learning on a large amount of low accuracy predicted logP values before finally tuning our model using a small, accurate dataset of 244 druglike compounds to create MRlogP, a neural network-based predictor of logP capable of outperforming state of the art freely available logP prediction methods for druglike small molecules. MRlogP achieves an average root mean squared error of 0.988 and 0.715 against druglike molecules from Reaxys and PHYSPROP. We have made the trained neural network predictor and all associated code for descriptor generation freely available. In addition, MRlogP may be used online via a web interface.
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Okolo EN, Ugwu DI, Ezema BE, Ndefo JC, Eze FU, Ezema CG, Ezugwu JA, Ujam OT. New chalcone derivatives as potential antimicrobial and antioxidant agent. Sci Rep 2021; 11:21781. [PMID: 34741131 PMCID: PMC8571407 DOI: 10.1038/s41598-021-01292-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 10/14/2021] [Indexed: 01/11/2023] Open
Abstract
Seven chalcone derivatives were synthesized by the Claisen-Schmidt condensation. The structures of the compounds were confirmed by spectral data (Ultraviolet/visible, infrared, nuclear magnetic resonance and mass spectroscopy). The compounds were tested for their in silico and in vitro antimicrobial and antioxidant activities. The molecular docking assessments showed that all the compounds exhibited good binding affinity with the target microorganism proteins but, compounds 6e and 6g showed better binding affinity compared with the standards. The antimicrobial test revealed that all the compounds screened were active against Staphylococcus aureus and Bacillus subtilis and had minimum inhibitory concentrations (MIC) between 0.4 and 0.6 mg/mL. Compounds 6a, 6c and 6d had moderate activities on Salmonella typhi. Compounds 6b and 6c had moderate activity on Escherichia coli. Compound 6c had moderate activity on Aspergillus niger while compounds 6a and 6e had poor activity. All the compounds except compound 6e had no inhibition against Pseudomonas aeruginosa. The in-vitro antioxidant activity was assessed using ethylenediaminetetraacetate (EDTA) as the standard. Compounds 6c, 6e and 6g gave excellent inhibitory activity better than the standard. Compound 6a gave good activity at 500 μg/mL and 1000 μg/mL concentrations but, below the standard at 250 μg/mL and no inhibition at 125 μg/mL. Compound 6d had good inhibition at 500 μg/mL and 1000 μg/mL but, no inhibition at 125 μg/mL and 250 μg/mL. Compound 6b was found to be inactive in all the concentrations. Absorption, distribution, metabolism and excretion properties of the compounds were assessed using SwissADME. The results of lead likeness showed that compound 6e is a lead-like molecule.
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Affiliation(s)
- Emelda N Okolo
- Department of Pure and Industrial Chemistry, University of Nigeria, Nsukka, Nigeria
| | - David I Ugwu
- Department of Pure and Industrial Chemistry, University of Nigeria, Nsukka, Nigeria.
| | - Benjamin E Ezema
- Department of Pure and Industrial Chemistry, University of Nigeria, Nsukka, Nigeria
| | - Joseph C Ndefo
- Department of Science Laboratory Technology, University of Nigeria, Nsukka, Nigeria
| | - Florence U Eze
- Department of Pure and Industrial Chemistry, University of Nigeria, Nsukka, Nigeria
| | - Chidimma G Ezema
- National Center for Energy Research and Development, University of Nigeria, Nsukka, Nigeria
| | - James A Ezugwu
- Department of Pure and Industrial Chemistry, University of Nigeria, Nsukka, Nigeria
| | - Oguejiofo T Ujam
- Department of Pure and Industrial Chemistry, University of Nigeria, Nsukka, Nigeria
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Truong J, George A, Holien JK. Analysis of physicochemical properties of protein-protein interaction modulators suggests stronger alignment with the "rule of five". RSC Med Chem 2021; 12:1731-1749. [PMID: 34778774 DOI: 10.1039/d1md00213a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 07/27/2021] [Indexed: 11/21/2022] Open
Abstract
Despite the important roles played by protein-protein interactions (PPIs) in disease, they have been long considered as 'undruggable'. However, recent advances have suggested that PPIs are druggable but may not follow conventional rules of 'drug ability'. Here we explore which physicochemical parameters are essential for a PPI modulator to be a clinical drug by analysing the physicochemical properties of small-molecule PPI modulators in the market, in clinical trials, and published. Our analysis reveals that those compounds currently on the market have a larger range of values for most of the physicochemical parameters, whereas those in clinical trials fit much more stringently to standard drug-like parameters. This observation was particularly true for molecular weight, clog P and topological polar surface area, where aside from a few outliers, most of the compounds in clinical trials fit within standard drug-like parameters. This implies that the newer PPI modulators are more drug-like than those currently on the market, suggesting that designing new PPI-specific screening libraries should remain within standard drug-like parameters in order to obtain a clinical candidate. Taken together, our analysis has important implications for designing future drug discovery campaigns aimed at targeting PPIs.
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Affiliation(s)
- Jia Truong
- STEM College, RMIT University Vic Australia
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35
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Sabat M, Dougan DR, Knight B, Lawson JD, Scorah N, Smith CR, Taylor ER, Vu P, Wyrick C, Wang H, Balakrishna D, Hixon M, Madakamutil L, McConn D. Discovery of the Bruton's Tyrosine Kinase Inhibitor Clinical Candidate TAK-020 ( S)-5-(1-((1-Acryloylpyrrolidin-3-yl)oxy)isoquinolin-3-yl)-2,4-dihydro-3 H-1,2,4-triazol-3-one, by Fragment-Based Drug Design. J Med Chem 2021; 64:12893-12902. [PMID: 34448571 DOI: 10.1021/acs.jmedchem.1c01026] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
This publication details the successful use of FBDD (fragment-based drug discovery) principles in the invention of a novel covalent Bruton's tyrosine kinase inhibitor, which ultimately became the Takeda Pharmaceuticals clinical candidate TAK-020. Described herein are the discovery of the fragment 5-phenyl-2,4-dihydro-3H-1,2,4-triazol-3-one, the subsequent optimization of this hit molecule to the candidate, and synthesis and performance in pharmacodynamic and efficacy models along with direct biophysical comparison of TAK-020 with other clinical-level assets and the marketed drug Ibrutinib.
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Affiliation(s)
- Mark Sabat
- Takeda California, 9625 Towne Centre Dr., San Diego, California 92121, United States
| | - Douglas R Dougan
- Takeda California, 9625 Towne Centre Dr., San Diego, California 92121, United States
| | - Beverly Knight
- Pfizer, 10777 Science Center Dr., San Diego, California 92121, United States
| | - J David Lawson
- Mirati Therapeutics, Inc., 9393 Towne Centre Dr. #200, San Diego, California 92121, United States
| | - Nicholas Scorah
- Takeda California, 9625 Towne Centre Dr., San Diego, California 92121, United States
| | - Christopher R Smith
- Mirati Therapeutics, Inc., 9393 Towne Centre Dr. #200, San Diego, California 92121, United States
| | - Ewan R Taylor
- Takeda California, 9625 Towne Centre Dr., San Diego, California 92121, United States
| | - Phong Vu
- Takeda California, 9625 Towne Centre Dr., San Diego, California 92121, United States
| | - Corey Wyrick
- Takeda California, 9625 Towne Centre Dr., San Diego, California 92121, United States
| | - Haixia Wang
- Takeda California, 9625 Towne Centre Dr., San Diego, California 92121, United States
| | - Deepika Balakrishna
- Takeda California, 9625 Towne Centre Dr., San Diego, California 92121, United States
| | - Mark Hixon
- VeriSIM Life, 1 Sansome Street Suite 3500, San Francisco, California 94104, United States
| | - Loui Madakamutil
- Invivoscribe Therapeutics, Inc., 10222 Barnes Canyon Rd., Bldg. 1, San Diego, California 92121, United States
| | - Donavon McConn
- Takeda California, 9625 Towne Centre Dr., San Diego, California 92121, United States
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36
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Rogawski R, Rogel A, Bloch I, Gal M, Horovitz A, London N, Sharon M. Intracellular Protein–Drug Interactions Probed by Direct Mass Spectrometry of Cell Lysates. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202104947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Rivkah Rogawski
- Department of Biomolecular Sciences Weizmann Institute of Science Rehovot 7610001 Israel
| | - Adi Rogel
- Department of Chemical and Structural Biology Weizmann Institute of Science Rehovot 7610001 Israel
| | - Itai Bloch
- Biotechnology Department MIGAL-Galilee Research Institute Kiryat-Shmona 11016 Israel
| | - Maayan Gal
- Department of Oral Biology The Goldschleger School of Dental Medicine Sackler Faculty of Medicine Tel Aviv University Tel Aviv 6997801 Israel
| | - Amnon Horovitz
- Department of Chemical and Structural Biology Weizmann Institute of Science Rehovot 7610001 Israel
| | - Nir London
- Department of Chemical and Structural Biology Weizmann Institute of Science Rehovot 7610001 Israel
| | - Michal Sharon
- Department of Biomolecular Sciences Weizmann Institute of Science Rehovot 7610001 Israel
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37
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Steverlynck J, Sitdikov R, Rueping M. The Deuterated "Magic Methyl" Group: A Guide to Site-Selective Trideuteromethyl Incorporation and Labeling by Using CD 3 Reagents. Chemistry 2021; 27:11751-11772. [PMID: 34076925 PMCID: PMC8457246 DOI: 10.1002/chem.202101179] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Indexed: 12/12/2022]
Abstract
In the field of medicinal chemistry, the precise installation of a trideuteromethyl group is gaining ever-increasing attention. Site-selective incorporation of the deuterated "magic methyl" group can provide profound pharmacological benefits and can be considered an important tool for drug optimization and development. This review provides a structured overview, according to trideuteromethylation reagent, of currently established methods for site-selective trideuteromethylation of carbon atoms. In addition to CD3 , the selective introduction of CD2 H and CDH2 groups is also considered. For all methods, the corresponding mechanism and scope are discussed whenever reported. As such, this review can be a starting point for synthetic chemists to further advance trideuteromethylation methodologies. At the same time, this review aims to be a guide for medicinal chemists, offering them the available C-CD3 formation strategies for the preparation of new or modified drugs.
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Affiliation(s)
- Joost Steverlynck
- Kaust Catalysis Center (KCC)King Abdullah University Science and Technology (KAUST)Thuwal23955-6900Saudi Arabia
| | - Ruzal Sitdikov
- Kaust Catalysis Center (KCC)King Abdullah University Science and Technology (KAUST)Thuwal23955-6900Saudi Arabia
| | - Magnus Rueping
- Kaust Catalysis Center (KCC)King Abdullah University Science and Technology (KAUST)Thuwal23955-6900Saudi Arabia
- Institute for Experimental Molecular ImagingRWTH Aachen UniversityForckenbeckstrasse 5552074Aachen
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38
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Rogawski R, Rogel A, Bloch I, Gal M, Horovitz A, London N, Sharon M. Intracellular Protein-Drug Interactions Probed by Direct Mass Spectrometry of Cell Lysates. Angew Chem Int Ed Engl 2021; 60:19637-19642. [PMID: 34101963 PMCID: PMC8457057 DOI: 10.1002/anie.202104947] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 05/23/2021] [Indexed: 12/22/2022]
Abstract
Understanding protein–ligand interactions in a cellular context is an important goal in molecular biology and biochemistry, and particularly for drug development. Investigators must demonstrate that drugs penetrate cells and specifically bind their targets. Towards that end, we present a native mass spectrometry (MS)‐based method for analyzing drug uptake and target engagement in eukaryotic cells. This method is based on our previously introduced direct‐MS method for rapid analysis of proteins directly from crude samples. Here, direct‐MS enables label‐free studies of protein–drug binding in human cells and is used to determine binding affinities of lead compounds in crude samples. We anticipate that this method will enable the application of native MS to a range of problems where cellular context is important, including protein–protein interactions, drug uptake and binding, and characterization of therapeutic proteins.
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Affiliation(s)
- Rivkah Rogawski
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Adi Rogel
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Itai Bloch
- Biotechnology Department, MIGAL-Galilee Research Institute, Kiryat-Shmona, 11016, Israel
| | - Maayan Gal
- Department of Oral Biology, The Goldschleger School of Dental Medicine, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Amnon Horovitz
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Nir London
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Michal Sharon
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
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39
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Asghar A, Tan YC, Zahoor M, Zainal Abidin SA, Yow YY, Khan E, Lahiri C. A scaffolded approach to unearth potential antibacterial components from epicarp of Malaysian Nephelium lappaceum L. Sci Rep 2021; 11:13859. [PMID: 34226594 PMCID: PMC8257635 DOI: 10.1038/s41598-021-92622-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 06/10/2021] [Indexed: 11/09/2022] Open
Abstract
The emergence and spread of antimicrobial resistance have been of serious concern to human health and the management of bacterial infectious diseases. Effective treatment of these diseases requires the development of novel therapeutics, preferably free of side effects. In this regard, natural products are frequently conceived to be potential alternative sources for novel antibacterial compounds. Herein, we have evaluated the antibacterial activity of the epicarp extracts of the Malaysian cultivar of yellow rambutan fruit (Nephelium lappaceum L.) against six pathogens namely, Bacillus subtilis, methicillin-resistant Staphylococcus aureus (MRSA), Streptococcus pyogenes, Pseudomonas aeruginosa, Klebsiella pneumoniae and Salmonella enterica. Among a series of solvent extracts, fractions of ethyl acetate and acetone have revealed significant activity towards all tested strains. Chemical profiling of these fractions, via HPLC, LC-MS and GC-MS, has generated a library of potentially bioactive compounds. Downstream virtual screening, pharmacological prediction, and receptor-ligand molecular dynamics simulation have eventually unveiled novel potential antibacterial compounds, which can be extracted for medicinal use. We report compounds like catechin, eplerenone and oritin-4-beta-ol to be computationally inhibiting the ATP-binding domain of the chaperone, DnaK of P. aeruginosa and MRSA. Thus, our work follows the objective to propose new antimicrobials capable of perforating the barrier of resistance posed by both the gram positives and the negatives.
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Affiliation(s)
- Ali Asghar
- Department of Biological Sciences, Sunway University, Petaling Jaya, Malaysia
| | - Yong Chiang Tan
- Department of Biological Sciences, Sunway University, Petaling Jaya, Malaysia
| | - Mohammad Zahoor
- Department of Biochemistry, University of Malakand, Chakdara, Pakistan
| | | | - Yoon-Yen Yow
- Department of Biological Sciences, Sunway University, Petaling Jaya, Malaysia
| | - Ezzat Khan
- Department of Chemistry, University of Bahrain, Sakhir, Bahrain
| | - Chandrajit Lahiri
- Department of Biological Sciences, Sunway University, Petaling Jaya, Malaysia.
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Meijer J, Lamoree M, Hamers T, Antignac JP, Hutinet S, Debrauwer L, Covaci A, Huber C, Krauss M, Walker DI, Schymanski EL, Vermeulen R, Vlaanderen J. An annotation database for chemicals of emerging concern in exposome research. ENVIRONMENT INTERNATIONAL 2021; 152:106511. [PMID: 33773387 DOI: 10.1016/j.envint.2021.106511] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 02/03/2021] [Accepted: 03/06/2021] [Indexed: 05/18/2023]
Abstract
BACKGROUND Chemicals of Emerging Concern (CECs) include a very wide group of chemicals that are suspected to be responsible for adverse effects on health, but for which very limited information is available. Chromatographic techniques coupled with high-resolution mass spectrometry (HRMS) can be used for non-targeted screening and detection of CECs, by using comprehensive annotation databases. Establishing a database focused on the annotation of CECs in human samples will provide new insight into the distribution and extent of exposures to a wide range of CECs in humans. OBJECTIVES This study describes an approach for the aggregation and curation of an annotation database (CECscreen) for the identification of CECs in human biological samples. METHODS The approach consists of three main parts. First, CECs compound lists from various sources were aggregated and duplications and inorganic compounds were removed. Subsequently, the list was curated by standardization of structures to create "MS-ready" and "QSAR-ready" SMILES, as well as calculation of exact masses (monoisotopic and adducts) and molecular formulas. The second step included the simulation of Phase I metabolites. The third and final step included the calculation of QSAR predictions related to physicochemical properties, environmental fate, toxicity and Absorption, Distribution, Metabolism, Excretion (ADME) processes and the retrieval of information from the US EPA CompTox Chemicals Dashboard. RESULTS All CECscreen database and property files are publicly available (DOI: https://doi.org/10.5281/zenodo.3956586). In total, 145,284 entries were aggregated from various CECs data sources. After elimination of duplicates and curation, the pipeline produced 70,397 unique "MS-ready" structures and 66,071 unique QSAR-ready structures, corresponding with 69,526 CAS numbers. Simulation of Phase I metabolites resulted in 306,279 unique metabolites. QSAR predictions could be performed for 64,684 of the QSAR-ready structures, whereas information was retrieved from the CompTox Chemicals Dashboard for 59,739 CAS numbers out of 69,526 inquiries. CECscreen is incorporated in the in silico fragmentation approach MetFrag. DISCUSSION The CECscreen database can be used to prioritize annotation of CECs measured in non-targeted HRMS, facilitating the large-scale detection of CECs in human samples for exposome research. Large-scale detection of CECs can be further improved by integrating the present database with resources that contain CECs (metabolites) and meta-data measurements, further expansion towards in silico and experimental (e.g., MassBank) generation of MS/MS spectra, and development of bioinformatics approaches capable of using correlation patterns in the measured chemical features.
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Affiliation(s)
- Jeroen Meijer
- Institute for Risk Assessment Sciences (IRAS), Utrecht University, Utrecht, the Netherlands; Department Environment & Health, Vrije Universiteit, Amsterdam, the Netherlands
| | - Marja Lamoree
- Department Environment & Health, Vrije Universiteit, Amsterdam, the Netherlands
| | - Timo Hamers
- Department Environment & Health, Vrije Universiteit, Amsterdam, the Netherlands
| | | | | | - Laurent Debrauwer
- Toxalim (Research Centre in Food Toxicology), Toulouse University, INRAE, ENVT, INP-Purpan, Toulouse, France; Metatoul-AXIOM Platform, National Infrastructure for Metabolomics and Fluxomics: MetaboHUB, Toxalim, INRAE, Toulouse, France
| | - Adrian Covaci
- Toxicological Center, University of Antwerp, Belgium
| | - Carolin Huber
- Department Effect-Directed Analysis, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Martin Krauss
- Department Effect-Directed Analysis, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Douglas I Walker
- Department of Environmental Medicine and Public Health, Icahn School of Medicine, Mount Sinai, New York, NY, USA
| | - Emma L Schymanski
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Roel Vermeulen
- Institute for Risk Assessment Sciences (IRAS), Utrecht University, Utrecht, the Netherlands
| | - Jelle Vlaanderen
- Institute for Risk Assessment Sciences (IRAS), Utrecht University, Utrecht, the Netherlands.
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Asghar A, Tan YC, Shahid M, Yow YY, Lahiri C. Metabolite Profiling of Malaysian Gracilaria edulis Reveals Eplerenone as Novel Antibacterial Compound for Drug Repurposing Against MDR Bacteria. Front Microbiol 2021; 12:653562. [PMID: 34276590 PMCID: PMC8279767 DOI: 10.3389/fmicb.2021.653562] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 05/06/2021] [Indexed: 11/13/2022] Open
Abstract
With a continuous threat of antimicrobial resistance on human health worldwide, efforts for new alternatives are ongoing for the management of bacterial infectious diseases. Natural products of land and sea, being conceived to be having fewer side effects, pose themselves as a welcome relief. In this respect, we have taken a scaffolded approach to unearthing the almost unexplored chemical constituents of Malaysian red seaweed, Gracilaria edulis. Essentially, a preliminary evaluation of the ethyl acetate and acetone solvent extracts, among a series of six such, revealed potential antibacterial activity against six MDR species namely, Klebsiella pneumoniae, Pseudomonas aeruginosa, Salmonella enterica, methicillin-resistant Staphylococcus aureus (MRSA), Streptococcus pyogenes, and Bacillus subtilis. Detailed analyses of the inlying chemical constituents, through LC-MS and GC-MS chromatographic separation, revealed a library of metabolic compounds. These were led for further virtual screening against selected key role playing proteins in the virulence of the aforesaid bacteria. To this end, detailed predictive pharmacological analyses added up to reinforce Eplerenone as a natural alternative from the plethora of plausible bioactives. Our work adds the ongoing effort to re-discover and repurpose biochemical compounds to combat the antimicrobial resistance offered by the Gram-positive and the -negative bacterial species.
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Affiliation(s)
- Ali Asghar
- Department of Biological Sciences, Sunway University, Petaling Jaya, Malaysia
| | - Yong-Chiang Tan
- Department of Biological Sciences, Sunway University, Petaling Jaya, Malaysia
| | - Muhammad Shahid
- Department of Food Sciences, Universiti Kebangsaan, Bangi, Malaysia
| | - Yoon-Yen Yow
- Department of Biological Sciences, Sunway University, Petaling Jaya, Malaysia
| | - Chandrajit Lahiri
- Department of Biological Sciences, Sunway University, Petaling Jaya, Malaysia
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42
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Leeson PD, Bento AP, Gaulton A, Hersey A, Manners EJ, Radoux CJ, Leach AR. Target-Based Evaluation of "Drug-Like" Properties and Ligand Efficiencies. J Med Chem 2021; 64:7210-7230. [PMID: 33983732 PMCID: PMC7610969 DOI: 10.1021/acs.jmedchem.1c00416] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Physicochemical descriptors commonly used to define "drug-likeness" and ligand efficiency measures are assessed for their ability to differentiate marketed drugs from compounds reported to bind to their efficacious target or targets. Using ChEMBL version 26, a data set of 643 drugs acting on 271 targets was assembled, comprising 1104 drug-target pairs having ≥100 published compounds per target. Taking into account changes in their physicochemical properties over time, drugs are analyzed according to their target class, therapy area, and route of administration. Recent drugs, approved in 2010-2020, display no overall differences in molecular weight, lipophilicity, hydrogen bonding, or polar surface area from their target comparator compounds. Drugs are differentiated from target comparators by higher potency, ligand efficiency (LE), lipophilic ligand efficiency (LLE), and lower carboaromaticity. Overall, 96% of drugs have LE or LLE values, or both, greater than the median values of their target comparator compounds.
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Affiliation(s)
- Paul D Leeson
- Paul Leeson Consulting Ltd, The Malt House, Main Street, Congerstone, Nuneaton, Warkwickshire CV13 6LZ, United Kingdom
| | - A Patricia Bento
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, United Kingdom
| | - Anna Gaulton
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, United Kingdom
| | - Anne Hersey
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, United Kingdom
| | - Emma J Manners
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, United Kingdom
| | - Chris J Radoux
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, United Kingdom
| | - Andrew R Leach
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SD, United Kingdom
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43
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Two Decades of 4D-QSAR: A Dying Art or Staging a Comeback? Int J Mol Sci 2021; 22:ijms22105212. [PMID: 34069090 PMCID: PMC8156896 DOI: 10.3390/ijms22105212] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/11/2021] [Accepted: 05/12/2021] [Indexed: 01/01/2023] Open
Abstract
A key question confronting computational chemists concerns the preferable ligand geometry that fits complementarily into the receptor pocket. Typically, the postulated ‘bioactive’ 3D ligand conformation is constructed as a ‘sophisticated guess’ (unnecessarily geometry-optimized) mirroring the pharmacophore hypothesis—sometimes based on an erroneous prerequisite. Hence, 4D-QSAR scheme and its ‘dialects’ have been practically implemented as higher level of model abstraction that allows the examination of the multiple molecular conformation, orientation and protonation representation, respectively. Nearly a quarter of a century has passed since the eminent work of Hopfinger appeared on the stage; therefore the natural question occurs whether 4D-QSAR approach is still appealing to the scientific community? With no intention to be comprehensive, a review of the current state of art in the field of receptor-independent (RI) and receptor-dependent (RD) 4D-QSAR methodology is provided with a brief examination of the ‘mainstream’ algorithms. In fact, a myriad of 4D-QSAR methods have been implemented and applied practically for a diverse range of molecules. It seems that, 4D-QSAR approach has been experiencing a promising renaissance of interests that might be fuelled by the rising power of the graphics processing unit (GPU) clusters applied to full-atom MD-based simulations of the protein-ligand complexes.
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Gong Q, Yu Q, Wang N, Hu J, Wang P, Yang F, Li T, You Q, Li X, Zhang X. Application of cation-π interactions in enzyme-substrate binding: Design, synthesis, biological evaluation, and molecular dynamics insights of novel hydrophilic substrates for NQO1. Eur J Med Chem 2021; 221:113515. [PMID: 33984806 DOI: 10.1016/j.ejmech.2021.113515] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 04/21/2021] [Accepted: 04/27/2021] [Indexed: 12/15/2022]
Abstract
Cation-π interaction is a type of noncovalent interaction formed between the π-electron system and the positively charged ion or moieties. In this study, we designed a series of novel NQO1 substrates by introducing aliphatic nitrogen-containing side chains to fit with the L-shaped pocket of NQO1 by the formation of cation-π interactions. Molecular dynamics (MD) simulation indicated that the basic N atom in the side chain of NQO1 substrates, which is prone to be protonated under physiological conditions, can form cation-π interactions with the Phe232 and Phe236 residues of the NQO1 enzyme. Compound 4 with a methylpiperazinyl substituent was identified as the most efficient substrate for NQO1 with the reduction rate and catalytic efficiency of 1263 ± 61 μmol NADPH/min/μmol NQO1 and 2.8 ± 0.3 × 106 M-1s-1, respectively. Notably, compound 4 exhibited increased water solubility (110 μg/mL) compared to that of β-lap (43 μg/mL), especially under acidic condition (pH = 3, solubility > 1000 μg/mL). Compound 4 (IC50/A549 = 2.4 ± 0.6 μM) showed potent antitumor activity against NQO1-rich cancer cells through ROS generation via NQO1-mediated redox cycling. These results emphasized that the application of cation-π interactions by introducing basic aliphatic amine moiety is beneficial for both the water solubility and the NQO1-substrate binding, leading to promising NQO1-targeting antitumor candidates with improved druglike properties.
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Affiliation(s)
- Qijie Gong
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 211198, China; Department of Chemistry, China Pharmaceutical University, Nanjing, 211198, China
| | - Quanwei Yu
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 211198, China; Department of Chemistry, China Pharmaceutical University, Nanjing, 211198, China
| | - Nan Wang
- Department of Medicinal Chemistry, College of Pharmacy, University of Minnesota-Twin Cities, Minneapolis, MN, USA
| | - Jiabao Hu
- Department of Chemistry, China Pharmaceutical University, Nanjing, 211198, China
| | - Pengfei Wang
- Department of Pharmaceutical Engineering, China Pharmaceutical University, Nanjing, 211198, China
| | - Fulai Yang
- Department of Chemistry, China Pharmaceutical University, Nanjing, 211198, China
| | - Tian Li
- Department of Pharmaceutical Engineering, China Pharmaceutical University, Nanjing, 211198, China
| | - Qidong You
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 211198, China.
| | - Xiang Li
- Department of Pharmaceutical Engineering, China Pharmaceutical University, Nanjing, 211198, China.
| | - Xiaojin Zhang
- Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 211198, China; Department of Chemistry, China Pharmaceutical University, Nanjing, 211198, China.
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Vohidov F, Andersen JN, Economides KD, Shipitsin MV, Burenkova O, Ackley JC, Vangamudi B, Nguyen HVT, Gallagher NM, Shieh P, Golder MR, Liu J, Dahlberg WK, Ehrlich DJC, Kim J, Kristufek SL, Huh SJ, Neenan AM, Baddour J, Paramasivan S, de Stanchina E, Kc G, Turnquist DJ, Saucier-Sawyer JK, Kopesky PW, Brady SW, Jessel MJ, Reiter LA, Chickering DE, Johnson JA, Blume-Jensen P. Design of BET Inhibitor Bottlebrush Prodrugs with Superior Efficacy and Devoid of Systemic Toxicities. J Am Chem Soc 2021; 143:4714-4724. [PMID: 33739832 DOI: 10.1021/jacs.1c00312] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Prodrugs engineered for preferential activation in diseased versus normal tissues offer immense potential to improve the therapeutic indexes (TIs) of preclinical and clinical-stage active pharmaceutical ingredients that either cannot be developed otherwise or whose efficacy or tolerability it is highly desirable to improve. Such approaches, however, often suffer from trial-and-error design, precluding predictive synthesis and optimization. Here, using bromodomain and extra-terminal (BET) protein inhibitors (BETi)-a class of epigenetic regulators with proven anticancer potential but clinical development hindered in large part by narrow TIs-we introduce a macromolecular prodrug platform that overcomes these challenges. Through tuning of traceless linkers appended to a "bottlebrush prodrug" scaffold, we demonstrate correlation of in vitro prodrug activation kinetics with in vivo tumor pharmacokinetics, enabling the predictive design of novel BETi prodrugs with enhanced antitumor efficacies and devoid of dose-limiting toxicities in a syngeneic triple-negative breast cancer murine model. This work may have immediate clinical implications, introducing a platform for predictive prodrug design and potentially overcoming hurdles in drug development.
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Affiliation(s)
- Farrukh Vohidov
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Jannik N Andersen
- XTuit Pharmaceuticals, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Kyriakos D Economides
- XTuit Pharmaceuticals, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Michail V Shipitsin
- XTuit Pharmaceuticals, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Olga Burenkova
- XTuit Pharmaceuticals, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - James C Ackley
- XTuit Pharmaceuticals, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Bhavatarini Vangamudi
- XTuit Pharmaceuticals, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Hung V-T Nguyen
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Nolan M Gallagher
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Peyton Shieh
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Matthew R Golder
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Jenny Liu
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States.,XTuit Pharmaceuticals, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - William K Dahlberg
- XTuit Pharmaceuticals, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Deborah J C Ehrlich
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Julie Kim
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Samantha L Kristufek
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Sung Jin Huh
- XTuit Pharmaceuticals, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Allison M Neenan
- XTuit Pharmaceuticals, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Joelle Baddour
- XTuit Pharmaceuticals, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | | | - Elisa de Stanchina
- Memorial Sloan Kettering Cancer Center, 417 E 68th St, New York, New York 10065, United States
| | - Gaurab Kc
- XTuit Pharmaceuticals, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - David J Turnquist
- XTuit Pharmaceuticals, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | | | - Paul W Kopesky
- XTuit Pharmaceuticals, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Samantha W Brady
- XTuit Pharmaceuticals, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Michael J Jessel
- XTuit Pharmaceuticals, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Lawrence A Reiter
- XTuit Pharmaceuticals, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Donald E Chickering
- XTuit Pharmaceuticals, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Jeremiah A Johnson
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Peter Blume-Jensen
- XTuit Pharmaceuticals, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
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Kos J, Kozik V, Pindjakova D, Jankech T, Smolinski A, Stepankova S, Hosek J, Oravec M, Jampilek J, Bak A. Synthesis and Hybrid SAR Property Modeling of Novel Cholinesterase Inhibitors. Int J Mol Sci 2021; 22:ijms22073444. [PMID: 33810550 PMCID: PMC8037530 DOI: 10.3390/ijms22073444] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/23/2021] [Accepted: 03/25/2021] [Indexed: 12/24/2022] Open
Abstract
A library of novel 4-{[(benzyloxy)carbonyl]amino}-2-hydroxybenzoic acid amides was designed and synthesized in order to provide potential acetyl- and butyrylcholinesterase (AChE/BChE) inhibitors; the in vitro inhibitory profile and selectivity index were specified. Benzyl(3-hydroxy-4-{[2-(trifluoromethoxy)phenyl]carbamoyl}phenyl)carbamate was the best AChE inhibitor with the inhibitory concentration of IC50 = 36.05 µM in the series, while benzyl{3-hydroxy-4-[(2-methoxyphenyl)carbamoyl]phenyl}-carbamate was the most potent BChE inhibitor (IC50 = 22.23 µM) with the highest selectivity for BChE (SI = 2.26). The cytotoxic effect was evaluated in vitro for promising AChE/BChE inhibitors. The newly synthesized adducts were subjected to the quantitative shape comparison with the generation of an averaged pharmacophore pattern. Noticeably, three pairs of fairly similar fluorine/bromine-containing compounds can potentially form the activity cliff that is manifested formally by high structure–activity landscape index (SALI) numerical values. The molecular docking study was conducted for the most potent AChE/BChE inhibitors, indicating that the hydrophobic interactions were overwhelmingly generated with Gln119, Asp70, Pro285, Thr120, and Trp82 aminoacid residues, while the hydrogen bond (HB)-donor ones were dominated with Thr120. π-stacking interactions were specified with the Trp82 aminoacid residue of chain A as well. Finally, the stability of chosen liganded enzymatic systems was assessed using the molecular dynamic simulations. An attempt was made to explain the noted differences of the selectivity index for the most potent molecules, especially those bearing unsubstituted and fluorinated methoxy group.
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Affiliation(s)
- Jiri Kos
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute, Palacky University, Slechtitelu 27, 78371 Olomouc, Czech Republic;
- Correspondence: (J.K.); (A.B.)
| | - Violetta Kozik
- Department of Chemistry, University of Silesia, Szkolna 9, 40007 Katowice, Poland;
| | - Dominika Pindjakova
- Department of Analytical Chemistry, Faculty of Natural Sciences, Comenius University, Ilkovicova 6, 84215 Bratislava, Slovakia; (D.P.); (T.J.)
| | - Timotej Jankech
- Department of Analytical Chemistry, Faculty of Natural Sciences, Comenius University, Ilkovicova 6, 84215 Bratislava, Slovakia; (D.P.); (T.J.)
- NT-LAB o.z., Teplicka 35, 92101 Piestany, Slovakia
| | - Adam Smolinski
- GiG Research Institute, Pl. Gwarkow 1, 40166 Katowice, Poland;
| | - Sarka Stepankova
- Department of Biological and Biochemical Sciences, Faculty of Chemical Technology, University of Pardubice, Studentska 573, 53210 Pardubice, Czech Republic;
| | - Jan Hosek
- Department of Pharmacology and Toxicology, Veterinary Research Institute, Hudcova 296/70, 62100 Brno, Czech Republic;
| | - Michal Oravec
- Global Change Research Institute CAS, Belidla 986/4a, 60300 Brno, Czech Republic;
| | - Josef Jampilek
- Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute, Palacky University, Slechtitelu 27, 78371 Olomouc, Czech Republic;
- Department of Analytical Chemistry, Faculty of Natural Sciences, Comenius University, Ilkovicova 6, 84215 Bratislava, Slovakia; (D.P.); (T.J.)
| | - Andrzej Bak
- Department of Chemistry, University of Silesia, Szkolna 9, 40007 Katowice, Poland;
- Correspondence: (J.K.); (A.B.)
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Bhutani P, Joshi G, Raja N, Bachhav N, Rajanna PK, Bhutani H, Paul AT, Kumar R. U.S. FDA Approved Drugs from 2015-June 2020: A Perspective. J Med Chem 2021; 64:2339-2381. [PMID: 33617716 DOI: 10.1021/acs.jmedchem.0c01786] [Citation(s) in RCA: 252] [Impact Index Per Article: 84.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In the present work, we report compilation and analysis of 245 drugs, including small and macromolecules approved by the U.S. FDA from 2015 until June 2020. Nearly 29% of the drugs were approved for the treatment of various types of cancers. Other major therapeutic areas of focus were infectious diseases (14%); neurological conditions (12%); and genetic, metabolic, and cardiovascular disorders (7-8% each). Itemization of the approved drugs according to the year of approval, sponsor, target, chemical class, major drug-metabolizing enzyme(s), route of administration/elimination, and drug-drug interaction liability (perpetrator or/and victim) is presented and discussed. An effort has been made to analyze the pharmacophores to identify the structural (e.g., aromatic, heterocycle, and aliphatic), elemental (e.g., boron, sulfur, fluorine, phosphorus, and deuterium), and functional group (e.g., nitro drugs) diversity among the approved drugs. Further, descriptor-based chemical space analysis of FDA approved drugs and several strategies utilized for optimizing metabolism leading to their discoveries have been emphasized. Finally, an analysis of drug-likeness for the approved drugs is presented.
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Affiliation(s)
- Priyadeep Bhutani
- Pharmaceutical Candidate Optimization, Biocon Bristol-Myers Squibb R&D Centre, Syngene International Limited, Bangalore 560099, India.,Department of Pharmacy, Birla Institute of Technology and Science (BITS) Pilani, Pilani Campus, Rajasthan 333031, India
| | - Gaurav Joshi
- Laboratory for Drug Design and Synthesis, Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Bathinda 151001, India
| | - Nivethitha Raja
- Pharmaceutical Candidate Optimization, Biocon Bristol-Myers Squibb R&D Centre, Syngene International Limited, Bangalore 560099, India
| | - Namrata Bachhav
- 1015 E Cozza Drive # 12, Spokane Washington 99208, United States
| | - Prabhakar K Rajanna
- Pharmaceutical Candidate Optimization, Biocon Bristol-Myers Squibb R&D Centre, Syngene International Limited, Bangalore 560099, India
| | - Hemant Bhutani
- Pharmaceutical Development, Biocon Bristol-Myers Squibb R&D Centre, Bristol-Myers Squibb India Private Limited, Bangalore 560099, India
| | - Atish T Paul
- Department of Pharmacy, Birla Institute of Technology and Science (BITS) Pilani, Pilani Campus, Rajasthan 333031, India
| | - Raj Kumar
- Laboratory for Drug Design and Synthesis, Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Bathinda 151001, India
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Responsible use of negative research outcomes-accelerating the discovery and development of new antibiotics. J Antibiot (Tokyo) 2021; 74:543-546. [PMID: 34272495 PMCID: PMC8390367 DOI: 10.1038/s41429-021-00439-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 05/21/2021] [Accepted: 06/08/2021] [Indexed: 02/06/2023]
Abstract
Failure to share and make use of existing knowledge, particularly negative research outcomes, has been recognized as one of the key sources of waste and inefficiency in the drug discovery and development process. In the field of antibiotic research, providing a platform where negative outcomes could be shared to prevent the vicious cycle of duplicating costly studies that produce the same negative results would greatly de-risk and accelerate the development of new antibiotics. Providing a legally supported framework that recognizes negative outcomes as intellectual contributions, which can subsequently be translated into a revenue-sharing model, may lead to more openness and value creation in support of a sustainable and responsible transformation of research into socially and economically beneficial innovations.
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Fullam E, Young RJ. Physicochemical properties and Mycobacterium tuberculosis transporters: keys to efficacious antitubercular drugs? RSC Med Chem 2020; 12:43-56. [PMID: 34041481 PMCID: PMC8130550 DOI: 10.1039/d0md00265h] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/15/2020] [Indexed: 12/14/2022] Open
Abstract
Securing novel, safe, and effective medicines to treat Mycobacterium tuberculosis remains an elusive goal, particularly influenced by the largely impervious Mtb envelope that limits exposure and thus efficacy of inhibitors at their cellular and periplasmic targets. The impact of physicochemical properties on pharmacokinetic parameters that govern oral absorption and exposure at sites of infection is considered alongside how these properties influence penetration of the Mtb envelope, with the likely influence of transporter proteins. The findings are discussed to benchmark current drugs and the emerging pipeline, whilst considering tactics for future rational and targeted design strategies, based around emerging data on Mtb transporters and their structures and functions.
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Affiliation(s)
- Elizabeth Fullam
- School of Life Sciences, University of Warwick Coventry CV4 7AL UK
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50
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Tomberg A, Boström J. Can easy chemistry produce complex, diverse, and novel molecules? Drug Discov Today 2020; 25:2174-2181. [DOI: 10.1016/j.drudis.2020.09.027] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 08/27/2020] [Accepted: 09/25/2020] [Indexed: 11/24/2022]
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