1
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Mosoh DA. Widely-targeted in silico and in vitro evaluation of veratrum alkaloid analogs as FAK inhibitors and dual targeting of FAK and Hh/SMO pathways for cancer therapy: A critical analysis. Int J Biol Macromol 2024:136201. [PMID: 39368576 DOI: 10.1016/j.ijbiomac.2024.136201] [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: 04/27/2024] [Revised: 09/26/2024] [Accepted: 09/29/2024] [Indexed: 10/07/2024]
Abstract
Focal Adhesive Kinase (FAK), a key player in aggressive cancers, mediates signals crucial for progression, invasion, and metastasis. Despite advances in targeted therapies, drug resistance is still a challenge, and survival rates remain low, particularly for late-stage patients, emphasizing the need for innovative cancer therapeutics. Cyclopamine, a veratrum alkaloid, has shown promising anti-tumor properties, but the search for more potent analogs with enhanced affinity for the biological target continues. This study employs a hybrid virtual screening approach combining pharmacophore model-based virtual screening (PB-VS) and docking-based virtual screening (DB-VS) to identify potential inhibitors of the FAK catalytic domain. PB-VS on the PubChem database yielded a set of hits, which were then docked with the FAK catalytic domain in two stages (1st and 2nd DB-VS). Hits were ranked based on docking scores and interactions with the active site. The top three compounds underwent molecular dynamics simulations, alongside two control compounds (SMO inhibitor(s) and FAK inhibitor(s)), to assess stability through RMSD, RMSF, Rg, and SASA analyses. ADMET properties were evaluated, and compounds were filtered based on drug-likeness criteria. Molecular dynamics simulations demonstrated the stability of compounds when complexed with the FAK catalytic domain. Compounds 16 (-25 kcal/mol), 88 (-27.47 kcal/mol), and 87 (-18.94 kcal/mol) exhibited comparable docking scores, interaction profiles, stability, and binding energies, indicating their potential as lead candidates. However, further validation and optimization through quantitative structure-activity relationship (QSAR) studies are essential to refine their efficacy and therapeutic potential. The in vitro cell-based assay demonstrated that compound 101PF, a FAK inhibitor, significantly inhibited the proliferation and migration of A549 cells. However, the results regarding the combined effects of FAK and SMO inhibitors were inconclusive, highlighting the need for further investigation. This study contributes to developing more effective anti-cancer drugs by improving the understanding of potential cyclopamine-based veratrum alkaloid analogs with enhanced interactions with the FAK catalytic domain.
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Affiliation(s)
- Dexter Achu Mosoh
- Centre for Biodiversity Exploration and Conservation (CBEC), 15, Kundan Residency, 4th Mile Mandla Road, Tilhari, Jabalpur, M.P 482021, India; Indian Institute of Technology Gandhinagar, Palaj Campus, Gujarat 382355, India; School of Science, Sanjeev Agrawal Global Educational (SAGE) University, Bhopal, M.P 462022, India; Prof. Wagner A. Vendrame's Laboratory, Environmental Horticulture Department, University of Florida, Institute of Food and Agricultural Sciences, 2550 Hull Rd., Gainesville, FL 32611, USA.
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2
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Gupta S, Vasanth D, Kumar A. Physicochemical analysis of chitosan oligosaccharide revealed its usefulness in effective delivery of drugs. JOURNAL OF BIOMATERIALS SCIENCE. POLYMER EDITION 2024:1-19. [PMID: 39169460 DOI: 10.1080/09205063.2024.2392365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Accepted: 08/09/2024] [Indexed: 08/23/2024]
Abstract
Chitosan oligosaccharides are biopolymers with a wide range of potential applications in various fields. This biopolymer is diverse and promising, and current research is investigating its capabilities for improved drug delivery. As chitosan oligosaccharide has the potential to be used as a drug delivery option, the purpose of this study was to examine its physicochemical characteristics and its potential for drug delivery. In this study, the pharmacokinetic properties of chitosan oligosaccharide were studied through Insilco investigation, which revealed that it is an extremely soluble and effective drug delivery candidate because it does not inhibit CYP isoenzymes and has a log Kp of -12.10 cm/s. It belongs to toxicity class 6 for acute oral toxicity, with an average similarity of 87.5% and a prediction accuracy of 70.97%. Additionally, XRD peak analysis revealed that the material was amorphous, as the peak appeared at 2θ = 24.62°, indicating the absence of well-defined crystalline areas. This characteristic makes the material more suitable for customization in many applications such as drug delivery and tissue engineering. FTIR, SEM, and TGA analysis were performed to gain a better understanding. These findings also emphasize the distinctive qualities and benefits of the oligosaccharides in this domain. Application of chitosan oligosaccharides in the development of efficient drug delivery systems. In the future, it would be more effective, targeted, and safe, with potent therapeutic efficacy for drug delivery.
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Affiliation(s)
- Shraddha Gupta
- Department of Biotechnology, National Institute of Technology, Raipur, India
| | | | - Awanish Kumar
- Department of Biotechnology, National Institute of Technology, Raipur, India
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3
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Yasser N, Sroor FM, El-Shorbagy HM, Eissa SM, Hassaneen HM, Abdelhamid IA. Synthesis, anticancer evaluation of novel hybrid pyrazole-based chalcones, molecular docking, DNA fragmentation, and gene expression: in vitro studies. RSC Adv 2024; 14:21859-21873. [PMID: 38984258 PMCID: PMC11232109 DOI: 10.1039/d4ra03375b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 07/03/2024] [Indexed: 07/11/2024] Open
Abstract
A unique series of pyrazolyl-chalcone derivatives was synthesized via the method of Claisen-Schmidt condensation. The desired chalcone derivatives 7a-d and 9a-f were obtained in good yields by reacting the 4-acetyl-5-thiophene-pyrazole with the appropriate heteroaryl aldehyde derivatives. The novel chalcones have undergone complete elemental analysis, 1H-NMR, 13C-NMR, mass spectrometry, and IR characterization. The three human cancer cell lines MCF7 (human Caucasian breast adenocarcinoma), PC3 (prostatic cancer) and PACA2 (pancreatic carcinoma) as well as the normal cell line BJ1 (normal skin fibroblasts) were tested in vitro for the anti-cancer properties of the newly synthesized chalcone derivatives. When compared to the reference medicine doxorubicin (IC50 = 52.1 μM), compound 9e showed the most promise derivative (IC50 = 27.6 μM) against PACA2 cells, while compound 7d demonstrated anticancer efficacy (IC50 = 42.6 μM against MCF7 cells compared to the reference drug doxorubicin (IC50 = 48 μM). Using breast and pancreatic cell lines, the gene expression, DNA damage, and DNA fragmentation percentages for compounds 7d and 9e were evaluated. Moreover, the molecular docking study of compounds 7d and 9e was assessed. The binding affinities of compound 9e toward P53 mutant Y220C was -22 kcal per mole, while those of compound 7d towards Bcl2 and CDK4 were -27.81 and -26.9 kcal per mole, respectively, compared to the standard values (-15.82, -33.96 and -29.9 kcal per mole).
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Affiliation(s)
- Norhan Yasser
- Department of Zoology, Faculty of Science, Cairo University 12613 Giza Egypt
- Faculty of Biotechnology, October University for Modern Science and Arts 6th October Giza Egypt
| | - Farid M Sroor
- Organometallic and Organometalloid Chemistry Department, National Research Centre 12622 Cairo Egypt
| | - Haidan M El-Shorbagy
- Department of Zoology, Faculty of Science, Cairo University 12613 Giza Egypt
- Faculty of Biotechnology, October University for Modern Science and Arts 6th October Giza Egypt
| | - Shaymaa M Eissa
- Department of Zoology, Faculty of Science, Cairo University 12613 Giza Egypt
| | - Hamdi M Hassaneen
- Department of Chemistry, Faculty of Science, Cairo University Giza Egypt
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4
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Ragheb MA, Mohamed FG, Diab HM, Ragab MS, Emara M, Elwahy AHM, Abdelhamid IA, Soliman MH. Novel Bis(2-cyanoacrylamide) Linked to Sulphamethoxazole: Synthesis, DNA Interaction, Anticancer, ADMET, Molecular Docking, and DFT Studies. Chem Biodivers 2024; 21:e202301341. [PMID: 38314957 DOI: 10.1002/cbdv.202301341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 01/27/2024] [Accepted: 02/01/2024] [Indexed: 02/07/2024]
Abstract
In the light of advancement and potential extensive use of medication design and therapy, new bis(cyanoacrylamides) incorporating sulphamethoxazole derivatives (7 a-7 f) were synthesized and confirmed by different spectral tools. In vitro anticancer activity towards different human cancer cells (HCT116, MDA-MB-231 and A549) was assessed using MTT assay. Among all derivatives, 4C- and 6C-spacer derivatives (7 e and 7 f) had the most potent growth inhibitory activities against HCT116 cells with IC50 values of 39.7 and 28.5 μM, respectively. 7 e and 7 f induced apoptosis and suppressed migration of HCT116 cells. These compounds also induced a significant increase in caspase-3 and CDH1 activities, and a downregulation of Bcl2 using ELISA. pBR322 DNA cleavage activities of cyanoacrylamides were determined using agarose gel electrophoresis. Furthermore, 7 e and 7 f showed good DNA and BSA binding affinities using different spectroscopic techniques. Furthermore, molecular docking for 7 e and 7 f was performed to anticipate their binding capabilities toward various proteins (Bcl2, CDH1 and BSA). The docking results were well correlated with those of experimental results. Additionally, density functional theory and ADMET study were performed to evaluate the molecular and pharmacokinetic features of 7 e and 7 f, respectively. Thus, this work reveals promising antitumor lead compounds that merit future research and activity enhancement.
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Affiliation(s)
- Mohamed A Ragheb
- Department of Chemistry (Biochemistry Division), Faculty of Science, Cairo University, Giza, 12613, Egypt
| | - Fatma G Mohamed
- Department of Chemistry (Biochemistry Division), Faculty of Science, Cairo University, Giza, 12613, Egypt
| | - Hadeer M Diab
- Department of Chemistry, Faculty of Science, Cairo University, Giza, 12613, Egypt
| | - Mona S Ragab
- Department of Chemistry, Faculty of Science, Cairo University, Giza, 12613, Egypt
| | - Marwan Emara
- Center for Aging and Associated Diseases, Zewail City of Science, Technology and innovation, 12578-, Giza, Egypt
| | - Ahmed H M Elwahy
- Department of Chemistry, Faculty of Science, Cairo University, Giza, 12613, Egypt
| | - Ismail A Abdelhamid
- Department of Chemistry, Faculty of Science, Cairo University, Giza, 12613, Egypt
| | - Marwa H Soliman
- Department of Chemistry (Biochemistry Division), Faculty of Science, Cairo University, Giza, 12613, Egypt
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5
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Khatoon H, Abdul Malek E, Faudzi SM, Rukayadi Y. Synthesis of a Series of Quinoxaline Derivatives and Their Antibacterial Effectiveness Against Pathogenic Bacteria. ChemistrySelect 2024; 9. [DOI: 10.1002/slct.202305073] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 01/24/2024] [Indexed: 08/18/2024]
Abstract
AbstractThe pharmacological importance of quinoxaline derivatives in antibacterial research is well recognized. This study focuses on the synthesis of new 2,3‐dichloroquinoxaline derivatives containing thioether/ether groups to explore their potential as potent antibacterial agents against various pathogenic bacteria. Most of the compounds exhibited significant antibacterial properties comparable to the standard drug chlorhexidine (CHX). The derivatives of 2‐chloro‐3‐(arylthiol)quinoxaline demonstrated efficacy against Escherichia coli with minimum inhibitory concentrations (MIC) of 2.5 mg/mL and minimum bactericidal concentrations (MBC) of 2.5 to 5.0 mg/mL. These derivatives also showed similar sensitivity to Bacillus pumilus. In addition, molecular docking simulations were performed to investigate the interaction between the synthesized compounds and the DNA gyrase protein (PDB ID: 1KZN), a target for antibiotics. Among the synthesized compounds, 2,3‐bis(3‐nitrophenoxy)quinoxaline exhibited the most favourable docking score of −8.36 kcal/mol, with a binding affinity comparable to that of the reference ligand clorobiocin (−9.3 kcal/mol).
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Affiliation(s)
- Hena Khatoon
- Department of Chemistry Faculty of Science Universiti Putra Malaysia Serdang 43400 Selangor Malaysia
| | - Emilia Abdul Malek
- Department of Chemistry Faculty of Science Universiti Putra Malaysia Serdang 43400 Selangor Malaysia
- Integrated Chemical BioPhysics Research Faculty of Science Universiti Putra Malaysia, Serdang 43400 Selangor Malaysia
| | - Siti Munirah Faudzi
- Department of Chemistry Faculty of Science Universiti Putra Malaysia Serdang 43400 Selangor Malaysia
- Department of Food Science Faculty of Food Science and technology Universiti Putra Malaysia Serdang 434000 Selangor Malaysia
| | - Yaya Rukayadi
- Department of Food Science Faculty of Food Science and technology Universiti Putra Malaysia Serdang 434000 Selangor Malaysia
- Natural Medicines and Product Research Laboratory Institute of Bioscience Universiti Putra Malaysia, Serdang 43400 Selangor Malaysia
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6
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Gonzalo-Navarro C, Zafon E, Organero JA, Jalón FA, Lima JC, Espino G, Rodríguez AM, Santos L, Moro AJ, Barrabés S, Castro J, Camacho-Aguayo J, Massaguer A, Manzano BR, Durá G. Ir(III) Half-Sandwich Photosensitizers with a π-Expansive Ligand for Efficient Anticancer Photodynamic Therapy. J Med Chem 2024; 67:1783-1811. [PMID: 38291666 PMCID: PMC10859961 DOI: 10.1021/acs.jmedchem.3c01276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 12/12/2023] [Accepted: 01/11/2024] [Indexed: 02/01/2024]
Abstract
One approach to reduce the side effects of chemotherapy in cancer treatment is photodynamic therapy (PDT), which allows spatiotemporal control of the cytotoxicity. We have used the strategy of coordinating π-expansive ligands to increase the excited state lifetimes of Ir(III) half-sandwich complexes in order to facilitate the generation of 1O2. We have obtained derivatives of formulas [Cp*Ir(C∧N)Cl] and [Cp*Ir(C∧N)L]BF4 with different degrees of π-expansion in the C∧N ligands. Complexes with the more π-expansive ligand are very effective photosensitizers with phototoxic indexes PI > 2000. Furthermore, PI values of 63 were achieved with red light. Time-dependent density functional theory (TD-DFT) calculations nicely explain the effect of the π-expansion. The complexes produce reactive oxygen species (ROS) at the cellular level, causing mitochondrial membrane depolarization, cleavage of DNA, nicotinamide adenine dinucleotide (NADH) oxidation, as well as lysosomal damage. Consequently, cell death by apoptosis and secondary necrosis is activated. Thus, we describe the first class of half-sandwich iridium cyclometalated complexes active in PDT.
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Affiliation(s)
- Carlos Gonzalo-Navarro
- Departamento
de Química Inorgánica, Orgánica y Bioquímica-
IRICA, Facultad de Ciencias y Tecnologías Químicas, Universidad de Castilla-La Mancha, Avda. C. J. Cela, 10, 13071 Ciudad Real, Spain
| | - Elisenda Zafon
- Departament
de Biologia, Facultat de Ciències, Universitat de Girona, Maria Aurèlia Capmany 40, 17003 Girona, Spain
| | - Juan Angel Organero
- Departamento
de Química Física, Facultad de Ciencias Ambientales
y Bioquímicas and INAMOL, Universidad
de Castilla-La Mancha, 45071 Toledo, Spain
| | - Félix A. Jalón
- Departamento
de Química Inorgánica, Orgánica y Bioquímica-
IRICA, Facultad de Ciencias y Tecnologías Químicas, Universidad de Castilla-La Mancha, Avda. C. J. Cela, 10, 13071 Ciudad Real, Spain
| | - Joao Carlos Lima
- LAQV-REQUIMTE,
Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Gustavo Espino
- Departamento
de Química, Facultad de Ciencias, Universidad de Burgos, Pza. Misael Bañuelos, s/n, 09001 Burgos, Spain
| | - Ana María Rodríguez
- Departamento
de Química Inorgánica, Orgánica y Bioquímica-
IRICA, Escuela Técnica Superior de Ingenieros Industriales, Universidad de Castilla-La Mancha, Avda. C. J. Cela, 3, 13071 Ciudad Real, Spain
| | - Lucía Santos
- Departamento
de Química Física, Facultad de Ciencias y Tecnologías
Químicas, Universidad de Castilla-La
Mancha, Avda. C. J. Cela,
s/n, 13071 Ciudad
Real, Spain
| | - Artur J. Moro
- LAQV-REQUIMTE,
Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Sílvia Barrabés
- Departament
de Biologia, Facultat de Ciències, Universitat de Girona, Maria Aurèlia Capmany 40, 17003 Girona, Spain
| | - Jessica Castro
- Departament
de Biologia, Facultat de Ciències, Universitat de Girona, Maria Aurèlia Capmany 40, 17003 Girona, Spain
| | - Javier Camacho-Aguayo
- Analytical
Chemistry Department, Analytic Biosensors Group, Instituto de Nanociencia
y Nanomateriales de Aragon, Faculty of Sciences, University of Zaragoza, 50009 Zaragoza, Spain
| | - Anna Massaguer
- Departament
de Biologia, Facultat de Ciències, Universitat de Girona, Maria Aurèlia Capmany 40, 17003 Girona, Spain
| | - Blanca R. Manzano
- Departamento
de Química Inorgánica, Orgánica y Bioquímica-
IRICA, Facultad de Ciencias y Tecnologías Químicas, Universidad de Castilla-La Mancha, Avda. C. J. Cela, 10, 13071 Ciudad Real, Spain
| | - Gema Durá
- Departamento
de Química Inorgánica, Orgánica y Bioquímica-
IRICA, Facultad de Ciencias y Tecnologías Químicas, Universidad de Castilla-La Mancha, Avda. C. J. Cela, 10, 13071 Ciudad Real, Spain
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7
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Dawood DH, Srour AM, Omar MA, Farghaly TA, El-Shiekh RA. Synthesis and molecular docking simulation of new benzimidazole-thiazole hybrids as cholinesterase inhibitors. Arch Pharm (Weinheim) 2024; 357:e2300201. [PMID: 37937360 DOI: 10.1002/ardp.202300201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 10/10/2023] [Accepted: 10/15/2023] [Indexed: 11/09/2023]
Abstract
Dementia is a cognitive disturbance that is generally correlated with central nervous system diseases, especially Alzheimer's disease. The limited number of medications available is insufficient to improve the lifestyle of the patients suffering from this disease. Thus, new benzimidazole-thiazole hybrids (3-10) were designed and synthesized as acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) inhibitory agents. The in vitro evaluation displayed that the derivatives 4b, 4d, 5b, 6a, 7a, and 8b demonstrated dual inhibitory efficiency against both AChE with IC50 ranging from 4.55 to 8.62 µM and BChE with IC50 ranging from 3.50 to 8.32 µM. By analyzing the Lineweaver-Burk plot, an uncompetitive form of inhibition was determined for the highly active compound 4d, revealing its inhibition type. The human telomerase reverse transcriptase-immortalized retinal pigment epithelial cell line was used to ensure the safety of the most potent cholinesterase inhibitors. Furthermore, compounds 4b, 4d, 5b, 6a, 7a, and 8b were evaluated for their neuroprotective and antioxidant properties, as well as their ability to suppress COX-2. The results demonstrated that compounds 4d, 5b, and 8b presented significant neuroprotection efficiency against H2 O2 -induced damage in SH-SY5Y cells with % cell viability of 67.42 ± 7.90%, 62.51 ± 6.71%, and 72.61 ± 8.10%, respectively, while the tested candidates did not reveal significant antioxidant activity. Otherwise, compounds 4b, 6a, 7a, and 8b displayed outstanding COX-2 inhibition effects with IC50 ranging from 0.050 to 0.080 μM relative to celecoxib (IC50 = 0.050 µM). In addition, molecular docking was carried out for the potent benzimidazole-thiazole hybrids with the active sites of both AChE (PDB ID: 4EY7) and BChE (PDB code: 1P0P). The tested candidates fit well in the active sites of both portions, with docking scores ranging from -8.65 to -6.64 kcal/mol (for AChE) and -8.71 to -7.73 kcal/mol (for BChE). In silico results show that the synthesized benzimidazole-thiazole hybrids have good physicochemical and pharmacokinetic properties with no Lipinski rule violations. The preceding results exhibited that compound 4d could be used as a new template for developing more significant cholinesterase inhibitors in the future.
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Affiliation(s)
- Dina H Dawood
- Chemistry of Natural and Microbial Products Department, Pharmaceutical and Drug Industries Research Institute, National Research Centre, Giza, Egypt
| | - Aladdin M Srour
- Department of Therapeutic Chemistry, National Research Centre, Giza, Egypt
| | - Mohamed A Omar
- Chemistry of Natural and Microbial Products Department, Pharmaceutical and Drug Industries Research Institute, National Research Centre, Giza, Egypt
| | - Thoraya A Farghaly
- Department of Chemistry, Faculty of Science, Cairo University, Giza, Egypt
| | - Riham A El-Shiekh
- Department of Pharmacognosy, Faculty of Pharmacy, Cairo University, Cairo, Egypt
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8
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Chowdhury H, Kumar Bera A, Subhasmita Raut S, Chandra Malick R, Sekhar Swain H, Saha A, Kumar Das B. In Vitro Antibacterial Efficacy of Cymbopogon flexuosus Essential Oil against Aeromonas hydrophila of Fish Origin and in Silico Molecular Docking of the Essential Oil Components against DNA Gyrase-B and Their Drug-Likeness. Chem Biodivers 2023; 20:e202200668. [PMID: 36799768 DOI: 10.1002/cbdv.202200668] [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: 07/21/2022] [Revised: 01/31/2023] [Accepted: 02/14/2023] [Indexed: 02/18/2023]
Abstract
In aquaculture, diseases caused by the Aeromonads with high antibiotic resistance are among the most common and troublesome diseases. Application of herbs is emerging as a tool in controlling these diseases. Plant extracts besides disease control, favor various physiological activities in fish. In this study, essential oil of Cymbopogon flexuosus (Poaceae family) was studied in vitro for its antibacterial efficacy against two oxytetracycline (OTC) resistant and one sensitive strains of Aeromonas hydrophila. The oil was found rich (86.93 %) in oxygenated terpenoids containing 74.15 % of citral. The oil exhibited dose dependent growth inhibition of the bacteria. Mean MIC value of the oil against the sensitive strain was recorded as 2.0 mg mL-1 whereas MBC value was recorded as 4.0 mg mL-1 . The oil was found effective against the OTC resistant isolates with the MIC and MBC values ranging from 2.67-3.33 and 4.0-6.67 mg mL-1 , respectively. In silico molecular docking of the essential oil components against DNA gyrase-B, a vital macromolecule in bacterial cell, was carried out to computationally asses the efficacy of the oil against the bacteria. Some of the components of the essential oil strongly bonded with the enzyme to inhibit its efficacy. Binding energy of some components of the oil was comparable to that of the conventional antibiotic, OTC. The identified phytochemicals exhibited favorable physicochemical and pharmacokinetic properties and satisfied the rule of five (Ro5).
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Affiliation(s)
- Hemanta Chowdhury
- ICAR - Central Inland Fisheries Research Institute, Manirampore, Barrackpore, Kolkata 700 120, West Bengal, India
| | - Asit Kumar Bera
- ICAR - Central Inland Fisheries Research Institute, Manirampore, Barrackpore, Kolkata 700 120, West Bengal, India
| | - Subhashree Subhasmita Raut
- ICAR - Central Inland Fisheries Research Institute, Manirampore, Barrackpore, Kolkata 700 120, West Bengal, India
| | - Ramesh Chandra Malick
- ICAR - Central Inland Fisheries Research Institute, Manirampore, Barrackpore, Kolkata 700 120, West Bengal, India
| | - Himanshu Sekhar Swain
- ICAR - Central Inland Fisheries Research Institute, Manirampore, Barrackpore, Kolkata 700 120, West Bengal, India
| | - Ajoy Saha
- ICAR - Central Inland Fisheries Research Institute, Manirampore, Barrackpore, Kolkata 700 120, West Bengal, India
| | - Basanta Kumar Das
- ICAR - Central Inland Fisheries Research Institute, Manirampore, Barrackpore, Kolkata 700 120, West Bengal, India
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9
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Zargar S, Wani TA, Rizwan Ahamad S. An Insight into Wheat Germ Oil Nutrition, Identification of Its Bioactive Constituents and Computer-Aided Multidimensional Data Analysis of Its Potential Anti-Inflammatory Effect via Molecular Connections. Life (Basel) 2023; 13:life13020526. [PMID: 36836883 PMCID: PMC9960255 DOI: 10.3390/life13020526] [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: 01/23/2023] [Revised: 02/09/2023] [Accepted: 02/13/2023] [Indexed: 02/17/2023] Open
Abstract
Wheat germ oil (WGO) is the richest source of unexplored antioxidants and anti-inflammatory compounds. In this study, we identified the constituents of WGO by gas chromatography-mass spectrometry (GC-MS). The physicochemical and pharmacokinetic behaviors were evaluated for the top 12 constituents with the common target FABP4. Three fatty acids with significant anti-inflammatory activity were evaluated for their interaction with FABP4 by molecular docking. The molecular mechanisms involved in anti-inflammatory responses were analyzed by various in-silico analytical tools and multidimensional data analysis. WGO showed anti-inflammatory activities via FABP4 interacting physically with target genes (77.84%) and by co-expressing with 8.01% genes. Primary targets for inflammatory pathways were PPARα, PPARγ, LPL, LEP, and ADIPOQ, as depicted by gene network enrichment analysis. The key pathways implicated were the metabolism of lipids, PPAR signaling, cellular response to alcohol, oxygen and nitrogen pathway, inflammatory response pathway, and regulation of the inflammatory pathway. The common transcription factors implicated were HNF1, AP2α, CEBP, FOX, STATS, MYC, Zic, etc. In this study, we found that WGO possesses anti-inflammatory potential via FABP4 binding to PPARα, PPARγ, LPL, LEP, and ADIPOQ gene expression by regulatory transcription factors HNF, AP2α, and CEPB.
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Affiliation(s)
- Seema Zargar
- Department of Biochemistry, College of Science, King Saud University, Riyadh 11495, Saudi Arabia
- Correspondence:
| | - Tanveer A. Wani
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Syed Rizwan Ahamad
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
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10
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Guerraoui A, Goudjil M, Direm A, Guerraoui A, Şengün İY, Parlak C, Djedouani A, Chelazzi L, Monti F, Lunedei E, Boumaza A. A rhodanine derivative as a potential antibacterial and anticancer agent: crystal structure, spectral characterization, DFT calculations, Hirshfeld surface analysis, in silico molecular docking and ADMET studies. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2023.135025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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11
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Mohamed SF, Elnaggar DH, Elsayed MA, Abd-Elghaffar HS, Hosny HM, Mohamed AM, Abbas EMH, Farghaly TA, El-Awady RA. Synthesis, Anticancer Activity, Pharmacokinetics, and Docking Study of Some New Heterocycles Linked Indole Moiety. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2151475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Salwa F. Mohamed
- Applied Organic Chemistry Department, National Research Centre, Dokki, Giza, Egypt
| | - Dina H. Elnaggar
- Applied Organic Chemistry Department, National Research Centre, Dokki, Giza, Egypt
| | - Mohamed A. Elsayed
- Applied Organic Chemistry Department, National Research Centre, Dokki, Giza, Egypt
| | | | - Hana M. Hosny
- Pesticide Chemistry Department, National Research Centre, Dokki, Giza, Egypt
| | - Ashraf M. Mohamed
- Applied Organic Chemistry Department, National Research Centre, Dokki, Giza, Egypt
| | - Eman M. H. Abbas
- Department of Chemistry, Natural and Microbial Products, National Research Center, Dokki, Cairo, Egypt
| | - Thoraya A. Farghaly
- Department of Chemistry, Faculty of Science, Cairo University, Cairo, Giza, Egypt
| | - Raafat A. El-Awady
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
- College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
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12
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Singh VK, Chaurasia H, Kumari P, Som A, Mishra R, Srivastava R, Naaz F, Singh A, Singh RK. Design, synthesis, and molecular dynamics simulation studies of quinoline derivatives as protease inhibitors against SARS-CoV-2. J Biomol Struct Dyn 2022; 40:10519-10542. [PMID: 34253149 DOI: 10.1080/07391102.2021.1946716] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
A new series of quinoline derivatives has been designed and synthesized as probable protease inhibitors (PIs) against severe acute respiratory syndrome coronavirus 2. In silico studies using DS v20.1.0.19295 software have shown that these compounds behaved as PIs while interacting at the allosteric site of target Mpro enzyme (6LU7). The designed compounds have shown promising docking results, which revealed that all compounds formed hydrogen bonds with His41, His164, Glu166, Tyr54, Asp187, and showed π-interaction with His41, the highly conserved amino acids in the target protein. Toxicity Prediction by Komputer Assisted Technology results confirmed that the compounds were found to be less toxic than the reference drug. Further, molecular dynamics simulations were performed on compound 5 and remdesivir with protease enzyme. Analysis of conformational stability, residue flexibility, compactness, hydrogen bonding, solvent accessible surface area (SASA), and binding free energy revealed comparable stability of protease:5 complex to the protease: remdesivir complex. The result of hydrogen bonding showed a large number of intermolecular hydrogen bonds formed between protein residues (Glu166 and Gln189) and ligand 5, indicating strong interaction, which validated the docking result. Further, compactness analysis, SASA and interactions like hydrogen-bonding demonstrated inhibitory properties of compound 5 similar to the existing reference drug. Thus, the designed compound 5 might act as a potential inhibitor against the protease enzyme.Communicated by Ramaswamy H. SarmaHighlightsQuinoline derivatives have been designed as protease inhibitors against SARS-CoV-2.The compounds were docked at the allosteric site of SARS-CoV-2-Mpro enzyme (PDB ID: 6LU7) to study the stability of protein-ligand complex.Docking studies indicated the stable ligand-protein complexes for all designed compounds.The Toxicity Prediction by Komputer Assisted Technology protocol in DS v20.1.0.19295 software was used to evaluate the toxicity of the designed quinoline derivatives.Molecular dynamics studies indicated the formation of stable ligand-Mpro complexes.
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Affiliation(s)
- Vishal K Singh
- Bioorganic Research Laboratory, Department of Chemistry, University of Allahabad, Prayagraj, India
| | - Himani Chaurasia
- Bioorganic Research Laboratory, Department of Chemistry, University of Allahabad, Prayagraj, India
| | - Priyanka Kumari
- Centre of Bioinformatics, University of Allahabad, Prayagraj, India
| | - Anup Som
- Centre of Bioinformatics, University of Allahabad, Prayagraj, India
| | - Richa Mishra
- Bioorganic Research Laboratory, Department of Chemistry, University of Allahabad, Prayagraj, India
| | - Ritika Srivastava
- Bioorganic Research Laboratory, Department of Chemistry, University of Allahabad, Prayagraj, India
| | - Farha Naaz
- Bioorganic Research Laboratory, Department of Chemistry, University of Allahabad, Prayagraj, India
| | - Anuradha Singh
- Bioorganic Research Laboratory, Department of Chemistry, University of Allahabad, Prayagraj, India
| | - Ramendra K Singh
- Bioorganic Research Laboratory, Department of Chemistry, University of Allahabad, Prayagraj, India
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13
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Omoboyowa DA, Kareem JA, Saibu OA, Bodun DS, Ajayi TM, Oyeneyin OE. Identification of Phyto-Compounds from Ilex kudingcha as Inhibitors of Sterol-14α-Demethylase Protease: A Computational Approach Against Chagas Disease. CHEMISTRY AFRICA 2022. [DOI: 10.1007/s42250-022-00565-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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14
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Velázquez-Jiménez R, González-Montiel S, Sánchez-Ortega I, Villagómez-Ibarra JR, Acevedo-Sandoval OA. ADMET prediction, Docking, DM analysis and antibacterial screening of epoxy furan-clerodanes from Croton hypoleucus. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.134840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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15
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Nature-Derived Compounds as Potential Bioactive Leads against CDK9-Induced Cancer: Computational and Network Pharmacology Approaches. Processes (Basel) 2022. [DOI: 10.3390/pr10122512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Given the importance of cyclin-dependent kinases (CDKs) in the maintenance of cell development, gene transcription, and other essential biological operations, CDK blockers have been generated to manage a variety of disorders resulting from CDK irregularities. Furthermore, CDK9 has a crucial role in transcription by regulating short-lived anti-apoptotic genes necessary for cancer cell persistence. Addressing CDK9 with blockers has consequently emerged as a promising treatment for cancer. This study scrutinizes the effectiveness of nature-derived compounds (geniposidic acid, quercetin, geniposide, curcumin, and withanolide C) against CDK9 through computational approaches. A molecular docking study was performed after preparing the protein and the ligands. The selected blockers of the CDK9 exerted reliable binding affinities (−8.114 kcal/mol to −13.908 kcal/mol) against the selected protein, resulting in promising candidates compared to the co-crystallized ligand (LCI). The binding affinity of geniposidic acid (−13.908 kcal/mol) to CDK9 is higher than quercetin (−10.775 kcal/mol), geniposide (−9.969 kcal/mol), curcumin (−9.898 kcal/mol), withanolide C (−8.114 kcal/mol), and the co-crystallized ligand LCI (−11.425 kcal/mol). Therefore, geniposidic acid is a promising inhibitor of CDK9. Moreover, the molecular dynamics studies assessed the structure–function relationships and protein–ligand interactions. The network pharmacology study for the selected ligands demonstrated the auspicious compound–target–pathway signaling pathways vital in developing tumor, tumor cell growth, differentiation, and promoting tumor cell progression. Moreover, this study concluded by analyzing the computational approaches the natural-derived compounds that have potential interacting activities against CDK9 and, therefore, can be considered promising candidates for CKD9-induced cancer. To substantiate this study’s outcomes, in vivo research is recommended.
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16
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Singh MB, Vishvakarma VK, Lal AA, Chandra R, Jain P, Singh P. A comparative study of 5- fluorouracil, doxorubicin, methotrexate, paclitaxel for their inhibition ability for Mpro of nCoV: Molecular docking and molecular dynamics simulations. J INDIAN CHEM SOC 2022. [PMCID: PMC9632266 DOI: 10.1016/j.jics.2022.100790] [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: 11/06/2022]
Abstract
A new corona virus (nCoV) is aetiological agent responsible for the viral pneumonia epidemic. Three is no specific therapeutic medicines available for the treatment of this condition and also effective treatment choices are few. In this work author tried to investigate some repurposing drug such as 5- fluorouracil, doxorubicin, methotrexate and paclitaxel against the main protease (Mpro) of nCoV by the computational model. Molecular docking was performed to screen out the best compound and doxorubicin was found to have minimum binding energy −121.89 kcal/mol. To further study, MD simulations were performed at 300 K and the result successfully corroborate the energy obtained by molecular docking. Temperature dependent MD simulation of the best molecule that is doxorubicin obtained from docking result was performed to check the variation in structural changes in Mpro of nCoV at 290 K, 310 K, 320 K and 325 K. It is sound that doxorubicin binds effectively with Mpro of nCoV at 290 K. Further ADME properties of the 5- fluorouracil, doxorubicin, methotrexate and paclitaxel were also evaluated to understand the bioavailability.
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17
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Al-Mijalli SH, Mrabti NN, Ouassou H, Sheikh RA, Abdallah EM, Assaggaf H, Bakrim S, Alshahrani MM, Awadh AAA, Qasem A, Attar A, Lee LH, Bouyahya A, Goh KW, Ming LC, Mrabti HN. Phytochemical Variability, In Vitro and In Vivo Biological Investigations, and In Silico Antibacterial Mechanisms of Mentha piperita Essential Oils Collected from Two Different Regions in Morocco. Foods 2022; 11:3466. [PMID: 36360079 PMCID: PMC9658668 DOI: 10.3390/foods11213466] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 10/20/2022] [Accepted: 10/24/2022] [Indexed: 08/13/2023] Open
Abstract
The objective of this work is to explore the phytochemical profile of Mentha piperita essential oils (MPEO) collected from two different Moroccan regions using gas chromatography-mass spectrophotometer (GC-MS) and to investigate their antioxidant, anti-inflammatory, antidiabetic and, antimicrobial effects using in vivo and in vitro assays. The chemical constituent of MPEO from the Azrou zone is dominated by carvone (70.25%), while MPEO from the Ouazzane zone is rich in Menthol (43.32%) and Menthone (29.4%). MPEO from Ouezzane showed higher antioxidant activity than EO from Azrou. Nevertheless, EO from Ouezzane considerably inhibited 5-Lipoxygenase (IC50 = 11.64 ± 0.02 µg/mL) compared to EO from Azro (IC50 = 23.84 ± 0.03 µg/mL). Both EOs from Azrou and Ouazzane inhibited the α-amylase activity in vitro, with IC50 values of 131.62 ± 0.01 µg/mL and 91.64 ± 0.03 µg/mL, respectively. The EOs were also tested for minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC). The discdiffusion test revealed that MPEOs from both regions have significant antibacterial efficacy, and MPEOs from the north region showed the highest effect. The gram-positive bacteria were the most susceptible organisms. The MIC concentrations were in the range of 0.05 to 6.25 mg/mL, and the MBC concentrations were within 0.05-25.0 mg/mL. The MBC/MIC index indicated that MPEO has strong bactericidal effects.
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Affiliation(s)
- Samiah Hamad Al-Mijalli
- Department of Biology, College of Sciences, Princess Nourah Bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Nidal Naceiri Mrabti
- Computer Chemistry and Modeling Team, Laboratory of Materials, Modeling and Environmental Engineering (LIMME), Faculty of Sciences Dhar El Mehraz, Sidi Mohamed Ben Abdellah University (USMBA), BP 1796, Atlas, Fez 30000, Morocco
| | - Hayat Ouassou
- Faculty of Sciences, University Mohammed First, Boulevard Mohamed VI BP 717, Oujda 60000, Morocco
| | - Ryan A. Sheikh
- Biochemistry Department, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Emad M. Abdallah
- Department of Science Laboratories, College of Science and Arts, Qassim University, Ar Rass 51921, Saudi Arabia
| | - Hamza Assaggaf
- Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Saad Bakrim
- Geo-Bio-Environment Engineering and Innovation Laboratory, Molecular Engineering, Biotechnology and Innovation Team, Polydisciplinary Faculty of Taroudant, Ibn Zohr University, Agadir 80000, Morocco
| | - Mohammed Merae Alshahrani
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Najran University, 1988, Najran 61441, Saudi Arabia
| | - Ahmed Abdullah Al Awadh
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Najran University, 1988, Najran 61441, Saudi Arabia
| | - Ahmed Qasem
- Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Ammar Attar
- Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Learn-Han Lee
- Novel Bacteria and Drug Discovery Research Group (NBDD), Microbiome and Bioresource Research Strength (MBRS), Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway 47500, Malaysia
| | - Abdelhakim Bouyahya
- Laboratory of Human Pathologies Biology, Department of Biology, Faculty of Sciences, Mohammed V University in Rabat, Rabat BP 6203, Morocco
| | - Khang Wen Goh
- Faculty of Data Science and Information Technology, INTI International University, Nilai 71800, Malaysia
| | - Long Chiau Ming
- Pengiran Anak Puteri Rashidah Sa’adatul Bolkiah Institute of Health Sciences, Universiti Brunei Darussalam, Gadong BE1410, Brunei
| | - Hanae Naceiri Mrabti
- Laboratoires TBC, Faculty of Pharmaceutical and Biological Sciences, B.P. 8359006 Lille, France
- Laboratory of Pharmacology and Toxicology, Bio Pharmaceutical and Toxicological Analysis Research Team, Faculty of Medicine and Pharmacy, University Mohammed V in Rabat, Rabat BP 6203, Morocco
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18
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Gupta A, Sahu N, Singh AP, Singh VK, Singh SC, Upadhye VJ, Mathew AT, Kumar R, Sinha RP. Exploration of Novel Lichen Compounds as Inhibitors of SARS-CoV-2 Mpro: Ligand-Based Design, Molecular Dynamics, and ADMET Analyses. Appl Biochem Biotechnol 2022; 194:6386-6406. [PMID: 35921031 PMCID: PMC9346229 DOI: 10.1007/s12010-022-04103-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/15/2022] [Indexed: 11/02/2022]
Abstract
In the year 2019-2020, the whole world witnessed the spread of a disease called COVID-19 caused by SARS-CoV-2. A number of effective drugs and vaccine has been formulated to combat this outbreak. For the development of anti-COVID-19 drugs, the main protease (Mpro) is considered a key target as it has rare mutations and plays a crucial role in the replication of the SARS CoV-2. In this study, a library of selected lichen compounds was prepared and used for virtual screening against SARS-CoV-2 Mpro using molecular docking, and several hits as potential inhibitors were identified. Remdesivir was used as a standard inhibitor of Mpro for its comparison with the identified hits. Twenty-six compounds were identified as potential hits against Mpro, and these were subjected to in silico ADMET property prediction, and the compounds having favorable properties were selected for further analysis. After manual inspection of their interaction with the binding pocket of Mpro and binding affinity score, four compounds, namely, variolaric acid, cryptostictinolide, gyrophoric acid, and usnic acid, were selected for molecular dynamics study to evaluate the stability of complex. The molecular dynamics results indicated that except cryptostictinolide, all the three compounds made a stable complex with Mpro throughout a 100-ns simulation time period. Among all, usnic acid seems to be more stable and effective against SARS-CoV-2 Mpro. In summary, our findings suggest that usnic acid, variolaric acid, and gyrophoric acid have potential to inhibit SARS-Cov-2 Mpro and act as a lead compounds for the development of antiviral drug candidates against SARS-CoV-2.
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Affiliation(s)
- Amit Gupta
- Laboratory of Photobiology and Molecular Microbiology, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
| | - Niharika Sahu
- Laboratory of Photobiology and Molecular Microbiology, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
| | - Ashish P Singh
- Laboratory of Photobiology and Molecular Microbiology, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
| | - Vinay Kumar Singh
- School of Biotechnology, Centre for Bioinformatics, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
| | - Suresh C Singh
- Pathkits Healthcare Pvt. Ltd, Electronic City Sector-18, Gurgaon, 122001, India
| | - Vijay J Upadhye
- Parul University (Waghodia), Vadodara, 391760, Gujarat, India
| | - Alen T Mathew
- Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (BHU), Varanasi, India
| | - Rajnish Kumar
- Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology (BHU), Varanasi, India
| | - Rajeshwar P Sinha
- Laboratory of Photobiology and Molecular Microbiology, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, India.
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19
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Anti-Inflammatory Potential of Fucoidan for Atherosclerosis: In Silico and In Vitro Studies in THP-1 Cells. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27103197. [PMID: 35630678 PMCID: PMC9146328 DOI: 10.3390/molecules27103197] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 05/12/2022] [Accepted: 05/13/2022] [Indexed: 01/13/2023]
Abstract
Several diseases, including atherosclerosis, are characterized by inflammation, which is initiated by leukocyte migration to the inflamed lesion. Hence, genes implicated in the early stages of inflammation are potential therapeutic targets to effectively reduce atherogenesis. Algal-derived polysaccharides are one of the most promising sources for pharmaceutical application, although their mechanism of action is still poorly understood. The present study uses a computational method to anticipate the effect of fucoidan and alginate on interactions with adhesion molecules and chemokine, followed by an assessment of the cytotoxicity of the best-predicted bioactive compound for human monocytic THP-1 macrophages by lactate dehydrogenase and crystal violet assay. Moreover, an in vitro pharmacodynamics evaluation was performed. Molecular docking results indicate that fucoidan has a greater affinity for L-and E-selectin, monocyte chemoattractant protein 1 (MCP-1), and intercellular adhesion molecule-1 (ICAM-1) as compared to alginate. Interestingly, there was no fucoidan cytotoxicity on THP-1 macrophages, even at 200 µg/mL for 24 h. The strong interaction between fucoidan and L-selectin in silico explained its ability to inhibit the THP-1 monocytes migration in vitro. MCP-1 and ICAM-1 expression levels in THP-1 macrophages treated with 50 µg/mL fucoidan for 24 h, followed by induction by IFN-γ, were shown to be significantly suppressed as eight- and four-fold changes, respectively, relative to cells treated only with IFN-γ. These results indicate that the electrostatic interaction of fucoidan improves its binding affinity to inflammatory markers in silico and reduces their expression in THP-1 cells in vitro, thus making fucoidan a good candidate to prevent inflammation.
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20
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Singh VK, Chaurasia H, Mishra R, Srivastava R, Naaz F, Kumar P, Singh RK. Docking, ADMET prediction, DFT analysis, synthesis, cytotoxicity, antibacterial screening and QSAR analysis of diarylpyrimidine derivatives. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131400] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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21
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Hasib RA, Ali MC, Rahman MS, Rahman MM, Ahmed FF, Mashud MAA, Islam MA, Jamal MAHM. A computational biology approach for the identification of potential SARS-CoV-2 main protease inhibitors from natural essential oil compounds. F1000Res 2021. [DOI: 10.12688/f1000research.73999.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has fomented a climate of fear worldwide due to its rapidly spreading nature, and high mortality rate. The World Health Organization (WHO) declared it as a global pandemic on 11th March, 2020. Many endeavors have been made to find appropriate medications to restrain the SARS CoV-2 infection from spreading but there is no specific antiviral therapy to date. However, a computer-aided drug design approach can be an alternative to identify probable drug candidates within a short time. SARS-CoV-2 main protease is a proven drug target, and it plays a pivotal role in viral replication and transcription. Methods: In this study, we identified a total of 114 essential oil compounds as a feasible anti-SARS-CoV-2 agent from several online reservoirs. These compounds were screened by incorporating ADMET profiling, molecular docking, and 50 ns of molecular dynamics simulation to identify potential drug candidates against the SARS-CoV-2 main protease. The crystallized SARS-CoV-2 main protease structure was collected from the RCSB PDB database (PDB ID 6LU7). Results: According to the results of the ADMET study, none of the compounds have any side effects that could reduce their druglikeness or pharmacokinetic properties. Out of 114 compounds, we selected bisabololoxide B, eremanthin, and leptospermone as our top drug candidates based on their higher binding affinity scores, and strong interaction with the Cys 145-His 41 catalytic dyad. Finally, the molecular dynamics simulation was implemented to evaluate the structural stability of the ligand-receptor complex. MD simulations disclosed that all the hits showed conformational stability compared to the positive control α-ketoamide. Conclusions: Our study showed that the top three hits might work as potential anti-SARS-CoV-2 agents, which can pave the way for discovering new drugs, but for experimental validation, they will require more in vivo trials.
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22
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Lampe JW, Alford JS, Boriak-Sjodin PA, Brach D, Cosmopoulos K, Duncan KW, Eckley ST, Foley MA, Harvey DM, Motwani V, Munchhof MJ, Raimondi A, Riera TV, Tang C, Thomenius MJ, Totman J, Farrow NA. Discovery of a First-in-Class Inhibitor of the Histone Methyltransferase SETD2 Suitable for Preclinical Studies. ACS Med Chem Lett 2021; 12:1539-1545. [PMID: 34671445 PMCID: PMC8521618 DOI: 10.1021/acsmedchemlett.1c00272] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 08/16/2021] [Indexed: 01/19/2023] Open
Abstract
![]()
SET domain-containing
protein 2 (SETD2), a histone methyltransferase,
has been identified as a target of interest in certain hematological
malignancies, including multiple myeloma. This account details the
discovery of EPZ-719, a novel and potent SETD2 inhibitor
with a high selectivity over other histone methyltransferases. A screening
campaign of the Epizyme proprietary histone methyltransferase-biased
library identified potential leads based on a 2-amidoindole core.
Structure-based drug design (SBDD) and drug metabolism/pharmacokinetics
(DMPK) optimization resulted in EPZ-719, an attractive
tool compound for the interrogation of SETD2 biology that enables in vivo target validation studies.
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Affiliation(s)
- John W. Lampe
- Epizyme Inc., 400 Technology Square, Fourth Floor, Cambridge, Massachusetts 02139, United States
| | - Joshua S. Alford
- Epizyme Inc., 400 Technology Square, Fourth Floor, Cambridge, Massachusetts 02139, United States
| | - P. Ann Boriak-Sjodin
- Epizyme Inc., 400 Technology Square, Fourth Floor, Cambridge, Massachusetts 02139, United States
| | - Dorothy Brach
- Epizyme Inc., 400 Technology Square, Fourth Floor, Cambridge, Massachusetts 02139, United States
| | - Kat Cosmopoulos
- Epizyme Inc., 400 Technology Square, Fourth Floor, Cambridge, Massachusetts 02139, United States
| | - Kenneth W. Duncan
- Epizyme Inc., 400 Technology Square, Fourth Floor, Cambridge, Massachusetts 02139, United States
| | - Sean T. Eckley
- Epizyme Inc., 400 Technology Square, Fourth Floor, Cambridge, Massachusetts 02139, United States
| | - Megan A. Foley
- Epizyme Inc., 400 Technology Square, Fourth Floor, Cambridge, Massachusetts 02139, United States
| | - Darren M. Harvey
- Epizyme Inc., 400 Technology Square, Fourth Floor, Cambridge, Massachusetts 02139, United States
| | - Vinny Motwani
- Epizyme Inc., 400 Technology Square, Fourth Floor, Cambridge, Massachusetts 02139, United States
| | - Michael J. Munchhof
- Epizyme Inc., 400 Technology Square, Fourth Floor, Cambridge, Massachusetts 02139, United States
| | - Alejandra Raimondi
- Epizyme Inc., 400 Technology Square, Fourth Floor, Cambridge, Massachusetts 02139, United States
| | - Thomas V. Riera
- Epizyme Inc., 400 Technology Square, Fourth Floor, Cambridge, Massachusetts 02139, United States
| | - Cuyue Tang
- Epizyme Inc., 400 Technology Square, Fourth Floor, Cambridge, Massachusetts 02139, United States
| | - Michael J. Thomenius
- Epizyme Inc., 400 Technology Square, Fourth Floor, Cambridge, Massachusetts 02139, United States
| | - Jennifer Totman
- Epizyme Inc., 400 Technology Square, Fourth Floor, Cambridge, Massachusetts 02139, United States
| | - Neil A. Farrow
- Epizyme Inc., 400 Technology Square, Fourth Floor, Cambridge, Massachusetts 02139, United States
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Lucas SCC, Atkinson SJ, Chung CW, Davis R, Gordon L, Grandi P, Gray JJR, Grimes T, Phillipou A, Preston AG, Prinjha RK, Rioja I, Taylor S, Tomkinson NCO, Wall I, Watson RJ, Woolven J, Demont EH. Optimization of a Series of 2,3-Dihydrobenzofurans as Highly Potent, Second Bromodomain (BD2)-Selective, Bromo and Extra-Terminal Domain (BET) Inhibitors. J Med Chem 2021; 64:10711-10741. [PMID: 34260229 DOI: 10.1021/acs.jmedchem.1c00344] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Herein, a series of 2,3-dihydrobenzofurans have been developed as highly potent bromo and extra-terminal domain (BET) inhibitors with 1000-fold selectivity for the second bromodomain (BD2) over the first bromodomain (BD1). Investment in the development of two orthogonal synthetic routes delivered inhibitors that were potent and selective but had raised in vitro clearance and suboptimal solubility. Insertion of a quaternary center into the 2,3-dihydrobenzofuran core blocked a key site of metabolism and improved the solubility. This led to the development of inhibitor 71 (GSK852): a potent, 1000-fold-selective, highly soluble compound with good in vivo rat and dog pharmacokinetics.
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Affiliation(s)
| | | | | | | | | | - Paola Grandi
- IVIVT Cellzome, Platform Technology and Science, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | | | | | | | | | | | | | | | - Nicholas C O Tomkinson
- WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, 259 Cathedral Street, Glasgow G1 1XL, U.K
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Arvidsson McShane S, Ahlberg E, Noeske T, Spjuth O. Machine Learning Strategies When Transitioning between Biological Assays. J Chem Inf Model 2021; 61:3722-3733. [PMID: 34152755 PMCID: PMC8317157 DOI: 10.1021/acs.jcim.1c00293] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Machine learning is widely used in drug development to predict activity in biological assays based on chemical structure. However, the process of transitioning from one experimental setup to another for the same biological endpoint has not been extensively studied. In a retrospective study, we here explore different modeling strategies of how to combine data from the old and new assays when training conformal prediction models using data from hERG and NaV assays. We suggest to continuously monitor the validity and efficiency of models as more data is accumulated from the new assay and select a modeling strategy based on these metrics. In order to maximize the utility of data from the old assay, we propose a strategy that augments the proper training set of an inductive conformal predictor by adding data from the old assay but only having data from the new assay in the calibration set, which results in valid (well-calibrated) models with improved efficiency compared to other strategies. We study the results for varying sizes of new and old assays, allowing for discussion of different practical scenarios. We also conclude that our proposed assay transition strategy is more beneficial, and the value of data from the new assay is higher, for the harder case of regression compared to classification problems.
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Affiliation(s)
- Staffan Arvidsson McShane
- Department of Pharmaceutical Biosciences and Science for Life Laboratory, Uppsala University, 751 24 Uppsala, Sweden
| | - Ernst Ahlberg
- Department of Pharmaceutical Biosciences and Science for Life Laboratory, Uppsala University, 751 24 Uppsala, Sweden.,Stena Line Scandinavia AB, AI & Data, 405 19 Gothenburg, Sweden.,Predictive Compound ADME & Safety, Drug Safety & Metabolism, AstraZeneca IMED Biotech Unit, 431 50 Gothenburg, Sweden
| | - Tobias Noeske
- Imaging and Data Analytics, Clinical Pharmacology & Safety Sciences, R&D, AstraZeneca, 431 50 Gothenburg, Sweden
| | - Ola Spjuth
- Department of Pharmaceutical Biosciences and Science for Life Laboratory, Uppsala University, 751 24 Uppsala, Sweden
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25
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Lansbergen B, Granatino P, Ritter T. Site-Selective C-H alkylation of Complex Arenes by a Two-Step Aryl Thianthrenation-Reductive Alkylation Sequence. J Am Chem Soc 2021; 143:7909-7914. [PMID: 34028272 PMCID: PMC8297726 DOI: 10.1021/jacs.1c03459] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Indexed: 12/28/2022]
Abstract
Herein, we present an undirected para-selective two-step C-H alkylation of complex arenes useful for late-stage functionalization. The combination of a site-selective C-H thianthrenation with palladium-catalyzed reductive electrophile cross-coupling grants access to a diverse range of synthetically useful alkylated arenes which cannot be accessed otherwise with comparable selectivity, diversity, and practicality. The robustness of this transformation is further demonstrated by thianthrenium-based reductive coupling of two complex fragments.
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Affiliation(s)
- Beatrice Lansbergen
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm Platz 1, D-45470 Mülheim an der
Ruhr, Germany
| | - Paola Granatino
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm Platz 1, D-45470 Mülheim an der
Ruhr, Germany
| | - Tobias Ritter
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm Platz 1, D-45470 Mülheim an der
Ruhr, Germany
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26
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Saito Y, Taniguchi Y, Hirazawa S, Miura Y, Tsurimoto H, Nakayoshi T, Oda A, Hamel E, Yamashita K, Goto M, Nakagawa-Goto K. Effects of substituent pattern on the intracellular target of antiproliferative benzo[b]thiophenyl chromone derivatives. Eur J Med Chem 2021; 222:113578. [PMID: 34171512 DOI: 10.1016/j.ejmech.2021.113578] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 05/09/2021] [Accepted: 05/19/2021] [Indexed: 11/30/2022]
Abstract
A new biological scaffold was produced by replacing the 6π-electron phenyl ring-B of a natural flavone skeleton with a 10π-electron benzothiophene (BT). Since aromatic rings are important for ligand protein interactions, this expansion of the π-electron system of ring-B might change the bioactivity profile. One of the resulting novel natural product-inspired compounds, 2-(benzo[b]thiophen-3-yl)-5-hydroxy-7-isopropoxy-6-methoxyflavone (6), effectively arrested the cell cycle at the G2/M phase and displayed significant antiproliferative effects with IC50 values of 0.05-0.08 μM against multiple human tumor cell lines, including a multidrug resistant line. A structure-activity relationship study revealed that a 10π-electron system with high aromaticity, juxtaposed 4-oxo and 5-hydroxy groups, and 7-alkoxy groups were important for potent antimitotic activity. Interestingly, two BT-flavonols (3-hydroxyflavone), 16 and 20, with 3-hydroxy and 5-alkoxy groups, induced distinct biological profiles affecting the cell cycle at the G1/S phase by inhibition of DNA replication through an interaction with topoisomerase I.
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Affiliation(s)
- Yohei Saito
- School of Pharmaceutical Sciences, College of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, 920-1192, Japan
| | - Yukako Taniguchi
- School of Pharmaceutical Sciences, College of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, 920-1192, Japan
| | - Sachika Hirazawa
- School of Pharmaceutical Sciences, College of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, 920-1192, Japan
| | - Yuta Miura
- School of Pharmaceutical Sciences, College of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, 920-1192, Japan
| | - Hiroyuki Tsurimoto
- School of Pharmaceutical Sciences, College of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, 920-1192, Japan
| | - Tomoki Nakayoshi
- Graduate School of Pharmacy, Meijo University, Tempaku-ku, Nagoya, 468-8503, Japan
| | - Akifumi Oda
- Graduate School of Pharmacy, Meijo University, Tempaku-ku, Nagoya, 468-8503, Japan
| | - Ernest Hamel
- Molecular Pharmacology Branch, Developmental Therapeutics Program, Division of Cancer Treatment and Diagnosis, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD, 21702, United States
| | - Katsumi Yamashita
- School of Pharmaceutical Sciences, College of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, 920-1192, Japan
| | - Masuo Goto
- Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27599-7568, United States.
| | - Kyoko Nakagawa-Goto
- School of Pharmaceutical Sciences, College of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, 920-1192, Japan; Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27599-7568, United States.
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27
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Radchenko DS, Naumchyk VS, Dziuba I, Kyrylchuk AA, Gubina KE, Moroz YS, Grygorenko OO. One-pot parallel synthesis of 1,3,5-trisubstituted 1,2,4-triazoles. Mol Divers 2021; 26:993-1004. [PMID: 33797670 DOI: 10.1007/s11030-021-10218-2] [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: 02/22/2021] [Accepted: 03/24/2021] [Indexed: 11/24/2022]
Abstract
An implementation of the three-component one-pot approach to unsymmetrical 1,3,5-trisubstituted-1,2,4-triazoles into combinatorial chemistry is described. The procedure is based on the coupling of amidines with carboxylic acids and subsequent cyclization with hydrazines. After the preliminary assessment of the reagent scope, the method had 81% success rate in parallel synthesis. It was shown that over a billion-sized chemical space of readily accessible ("REAL") compounds may be generated based on the proposed methodology. Analysis of physicochemical parameters shows that the library contains significant fractions of both drug-like and "beyond-rule-of-five" members. More than 10 million of accessible compounds meet the strictest lead-likeness criteria. Additionally, 195 Mln of sp3-enriched compounds can be produced. This makes the proposed approach a valuable tool in medicinal chemistry.
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Affiliation(s)
- Dmytro S Radchenko
- Enamine Ltd., Chervonotkatska Street 78, Kyiv, 02094, Ukraine.,Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyiv, 01601, Ukraine
| | | | - Igor Dziuba
- Chemspace, Chervonotkatska Street 78, Kyiv, 02094, Ukraine
| | - Andrii A Kyrylchuk
- Enamine Ltd., Chervonotkatska Street 78, Kyiv, 02094, Ukraine.,Institute of Organic Chemistry, National Academy of Sciences of Ukraine, Murmanska Street 5, Kyiv, 02094, Ukraine
| | - Kateryna E Gubina
- Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyiv, 01601, Ukraine
| | - Yurii S Moroz
- Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyiv, 01601, Ukraine.,Chemspace, Chervonotkatska Street 78, Kyiv, 02094, Ukraine
| | - Oleksandr O Grygorenko
- Enamine Ltd., Chervonotkatska Street 78, Kyiv, 02094, Ukraine. .,Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyiv, 01601, Ukraine.
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28
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Alnajjar R, Mohamed N, Kawafi N. Bicyclo[1.1.1]Pentane as Phenyl Substituent in Atorvastatin Drug to improve Physicochemical Properties: Drug-likeness, DFT, Pharmacokinetics, Docking, and Molecular Dynamic Simulation. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2020.129628] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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29
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Ma S, McGann M, Enyedy IJ. The influence of calculated physicochemical properties of compounds on their ADMET profiles. Bioorg Med Chem Lett 2021; 36:127825. [PMID: 33508464 DOI: 10.1016/j.bmcl.2021.127825] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/21/2020] [Accepted: 01/19/2021] [Indexed: 11/19/2022]
Abstract
We analyzed the influence of calculated physicochemical properties of more than 20,000 compounds on their P-gp and BCRP mediated efflux, microsomal stability, hERG inhibition, and plasma protein binding. Our goal was to provide guidance for designing compounds with desired pharmacokinetic profiles. Our analysis showed that compounds with ClogP less than 3 and molecular weight less than 400 will have high microsomal stability and low plasma protein binding. Compounds with logD less than 2.2 and/or basic pKa larger than 5.3 are likely to be BCRP substrates and compounds with basic pKa less than 5.2 and/or acidic pKa less than 13.4 are less likely to inhibit hERG. Based on these results, compounds with MW < 400, ClogP < 3, basic pKa < 5.2 and acidic pKa < 13.4 are likely to have good bioavailability and low hERG inhibition.
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MESH Headings
- ATP Binding Cassette Transporter, Subfamily B, Member 1/chemistry
- ATP Binding Cassette Transporter, Subfamily B, Member 1/metabolism
- ATP Binding Cassette Transporter, Subfamily G, Member 2/chemistry
- ATP Binding Cassette Transporter, Subfamily G, Member 2/metabolism
- Animals
- Blood Proteins/chemistry
- Blood Proteins/metabolism
- Chemistry, Physical
- Dose-Response Relationship, Drug
- Ether-A-Go-Go Potassium Channels/antagonists & inhibitors
- Ether-A-Go-Go Potassium Channels/genetics
- Ether-A-Go-Go Potassium Channels/metabolism
- Humans
- Mice
- Microsomes/chemistry
- Microsomes/metabolism
- Molecular Structure
- Molecular Weight
- Neoplasm Proteins/chemistry
- Neoplasm Proteins/metabolism
- Pharmaceutical Preparations/chemistry
- Rats
- Structure-Activity Relationship
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Affiliation(s)
- Shifan Ma
- Medicinal Chemistry, Biotherapeutic and Medicinal Science Department, Biogen, 225 Binney Street, Cambridge, MA 02142, United States
| | - Mark McGann
- OpenEye Scientific, Santa Fe, NM 87507, United States
| | - Istvan J Enyedy
- Medicinal Chemistry, Biotherapeutic and Medicinal Science Department, Biogen, 225 Binney Street, Cambridge, MA 02142, United States.
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30
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Elkwafi G, Mohamed N, Elabbar F, Alnajjar R. Flavonoid content of the Libyan Onosma Cyrenaicum: isolation, identification, electronic chemical reactivity, drug likeness, docking, and MD study. J Biomol Struct Dyn 2021; 40:7351-7366. [PMID: 33685329 DOI: 10.1080/07391102.2021.1897046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In this work, an attempt to identify the flavonoid content of the Libyan Onosma Cyrenaicum led to the isolation of three flavonoids 7,8-dihydroxy-2-(4-hydroxyphenyl)-4H-chromen-4-one(GE-001), 5,7-dihydroxy-2-(3-hydroxy-4-methoxy phenyl)-4H-chromen-4-one (GE-002) and 5,7-dihydroxy-3-(4-hydroxyphenyl)-4H-chromen-4-one (GE-003), the isolated compounds were characterized using 1H and 13C-NMR techniques. A further DFT study at ωB97-XD with 6-311++G** basis set in water was conducted to calculate the isolated compounds' global and local reactivity descriptors and Fukui indices along with their antioxidant activity. The drug-likeness and bioactivity properties of the isolated compounds were estimated and discussed. Finally, GE-001, GE-002, and GE-003 were docked into HCV NS5B polymerase active siteand this was followed by molecular dynamic simulation to certify the obtained docking result and to obtain the MM-GBSA free binding energyy of the isolated compounds. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ghazala Elkwafi
- Department of Chemistry, Faculty of Science, University of Benghazi, Benghazi, Libya
| | - Najwa Mohamed
- Department of Medicinal Chemistry, Faculty of Pharmacy, University of Benghazi, Benghazi, Libya
| | - Fakhri Elabbar
- Department of Chemistry, Faculty of Science, University of Benghazi, Benghazi, Libya
| | - Radwan Alnajjar
- Department of Chemistry, Faculty of Science, University of Benghazi, Benghazi, Libya.,Department of Chemistry, University of Cape Town, Rondebosch, South Africa
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31
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Chatzopoulou M, Emer E, Lecci C, Rowley JA, Casagrande AS, Moir L, Squire SE, Davies SG, Harriman S, Wynne GM, Wilson FX, Davies KE, Russell AJ. Decreasing HepG2 Cytotoxicity by Lowering the Lipophilicity of Benzo[d]oxazolephosphinate Ester Utrophin Modulators. ACS Med Chem Lett 2020; 11:2421-2427. [PMID: 33335663 DOI: 10.1021/acsmedchemlett.0c00405] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 10/26/2020] [Indexed: 12/11/2022] Open
Abstract
Utrophin modulation is a disease-modifying therapeutic strategy for Duchenne muscular dystrophy that would be applicable to all patient populations. To improve the suboptimal profile of ezutromid, the first-in-class clinical candidate, a second generation of utrophin modulators bearing a phosphinate ester moiety was developed. This modification significantly improved the physicochemical and ADME properties, but one of the main lead molecules was found to have dose-limiting hepatotoxicity. In this work we describe how less lipophilic analogues retained utrophin modulatory activity in a reporter gene assay, upregulated utrophin protein in dystrophic mouse muscle cells, but also had improved physicochemical and ADME properties. Notably, ClogP was found to directly correlate with pIC50 in HepG2 cells, hence leading to a potentially safer toxicological profiles in this series. Compound 21 showed a balanced profile (H2K EC50: 4.17 μM, solubility: 477 μM, mouse hepatocyte T 1/2 > 240 min) and increased utrophin protein 1.6-fold in a Western blot assay.
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Affiliation(s)
- Maria Chatzopoulou
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, U.K
| | - Enrico Emer
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, U.K
| | - Cristina Lecci
- Evoetec (U.K.) Ltd, 114 Innovation Drive, Milton Park, Milton, Abingdon OX14 4RZ, U.K
| | - Jessica A. Rowley
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, U.K
| | | | - Lee Moir
- MDUK Oxford Neuromuscular Centre, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, U.K
| | - Sarah E. Squire
- MDUK Oxford Neuromuscular Centre, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, U.K
| | - Stephen G. Davies
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, U.K
| | - Shawn Harriman
- Summit Therapeutics plc, 136a Eastern Avenue, Milton Park, Abingdon, Oxfordshire OX14 4SB, U.K
| | - Graham M. Wynne
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, U.K
| | - Francis X. Wilson
- Summit Therapeutics plc, 136a Eastern Avenue, Milton Park, Abingdon, Oxfordshire OX14 4SB, U.K
| | - Kay E. Davies
- MDUK Oxford Neuromuscular Centre, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, U.K
| | - Angela J. Russell
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford OX1 3TA, U.K
- Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3PQ, U.K
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32
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Janse van Rensburg HD, Legoabe LJ, Terre’Blanche G. C3 amino-substituted chalcone derivative with selective adenosine rA 1 receptor affinity in the micromolar range. CHEMICKE ZVESTI 2020; 75:1581-1605. [PMID: 33223599 PMCID: PMC7670844 DOI: 10.1007/s11696-020-01414-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 11/03/2020] [Indexed: 12/12/2022]
Abstract
ABSTRACT To identify novel adenosine receptor (AR) ligands based on the chalcone scaffold, herein the synthesis, characterization and in vitro and in silico evaluation of 33 chalcones (15-36 and 37-41) and structurally related compounds (42-47) are reported. These compounds were characterized by radioligand binding and GTP shift assays to determine the degree and type of binding affinity, respectively, against rat (r) A1 and A2A ARs. The chalcone derivatives 24, 29, 37 and 38 possessed selective A1 affinity below 10 µM, and thus, are the most active compounds of the present series; compound 38 was the most potent selective A1 AR antagonist (K i (r) = 1.6 µM). The structure-affinity relationships (SAR) revealed that the NH2-group at position C3 of ring A of the chalcone scaffold played a key role in affinity, and also, the Br-atom at position C3' on benzylidene ring B. Upon in vitro and in silico evaluation, the novel C3 amino-substituted chalcone derivative 38-that contains an α,ß-unsaturated carbonyl system and easily allows structural modification-may possibly be a synthon in future drug discovery. GRAPHIC ABSTRACT C3 amino-substituted chalcone derivative (38) with C3' Br substitution on benzylidene ring B possesses selective adenosine rA1 receptor affinity in micromolar range.
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Affiliation(s)
- Helena D. Janse van Rensburg
- Centre of Excellence for Pharmaceutical Sciences, North-West University, Private Bag X6001, Potchefstroom, 2520 South Africa
| | - Lesetja J. Legoabe
- Centre of Excellence for Pharmaceutical Sciences, North-West University, Private Bag X6001, Potchefstroom, 2520 South Africa
| | - Gisella Terre’Blanche
- Centre of Excellence for Pharmaceutical Sciences, North-West University, Private Bag X6001, Potchefstroom, 2520 South Africa
- Pharmaceutical Chemistry, School of Pharmacy, North-West University, Private Bag X6001, Potchefstroom, 2520 South Africa
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33
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Mutisya JM, Mobegi VA, Kinyua JK, Kivecu MN, Okoth RO, Chemwor GC, Mwakio EW, Cheruiyot AC, Yeda RA, Okello CO, Juma JA, Opot BH, Juma DW, Roth AL, Akala HM, Andagalu BM. Characterization of sulfated polysaccharide activity against virulent Plasmodium falciparum PHISTb/RLP1 protein. F1000Res 2020; 9:1268. [PMID: 35600144 PMCID: PMC9096147 DOI: 10.12688/f1000research.26756.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/19/2022] [Indexed: 11/20/2022] Open
Abstract
Background: The emergence of artemisinin resistance in South East Asia calls for urgent discovery of new drug compounds that have antiplasmodial activity. Unlike the classical compound screening drug discovery methods, the rational approach involving targeted drug discovery is less cumbersome and therefore key for innovation of new antiplasmodial compounds. Plasmodium falciparum (Pf) utilizes the process of host erythrocyte remodeling using Plasmodium-helical interspersed sub-telomeric domain (PHIST) containing proteins, which are amenable drug targets. The aim of this study is to identify inhibitors of PHIST from sulfated polysaccharides as new antimalarials. Methods: 251 samples from an ongoing study of epidemiology of malaria and drug resistance sensitivity patterns in Kenya were sequenced for PHISTb/RLP1 gene using Sanger sequencing. The sequenced reads were mapped to the reference Pf3D7 protein sequence of PHISTb/RLP1 using CLC Main Workbench. Homology modeling of both reference and mutant protein structures was achieved using the LOMETs tool. The models were refined using ModRefiner for energy minimization. Ramachandran plot was generated by ProCheck to assess the conformation of amino acids in the protein model. Protein binding sites predictions were assessed using FT SITE software. We searched for prospective antimalarials from PubChem. Docking experiments were achieved using AutoDock Vina and analysis results visualized in PyMOL. Results: Sanger sequencing generated 86 complete sequences. Upon mapping of the sequences to the reference, 12 non-synonymous single nucleotide polymorphisms were considered for mutant protein structure analysis. Eleven drug compounds with antiplasmodial activity were identified. Both modeled PHISTb/RLP1 reference and mutant structures had a Ramachandran score of >90% of the amino acids in the favored region. Ten of the drug compounds interacted with amino acid residues in PHISTb and RESA domains, showing potential activity against these proteins. Conclusion: This research identifies inhibitors of exported proteins that can be used in in vitro tests against the Plasmodium parasite.
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Affiliation(s)
- Jennifer M. Mutisya
- Department of Emerging and Infectious Diseases (DEID), United States Army Medical Research Directorate-Africa (USAMRD-A), Kenya Medical Research Institute (KEMRI)/Walter Reed Project, Kisumu, Kenya
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Victor A. Mobegi
- Department of Biochemistry, University of Nairobi, Nairobi, Kenya
| | - Johnson K. Kinyua
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Martha N. Kivecu
- Department of Emerging and Infectious Diseases (DEID), United States Army Medical Research Directorate-Africa (USAMRD-A), Kenya Medical Research Institute (KEMRI)/Walter Reed Project, Kisumu, Kenya
| | - Raphael O. Okoth
- Department of Emerging and Infectious Diseases (DEID), United States Army Medical Research Directorate-Africa (USAMRD-A), Kenya Medical Research Institute (KEMRI)/Walter Reed Project, Kisumu, Kenya
| | - Gladys C. Chemwor
- Department of Emerging and Infectious Diseases (DEID), United States Army Medical Research Directorate-Africa (USAMRD-A), Kenya Medical Research Institute (KEMRI)/Walter Reed Project, Kisumu, Kenya
| | - Edwin W. Mwakio
- Department of Emerging and Infectious Diseases (DEID), United States Army Medical Research Directorate-Africa (USAMRD-A), Kenya Medical Research Institute (KEMRI)/Walter Reed Project, Kisumu, Kenya
| | - Agnes C. Cheruiyot
- Department of Emerging and Infectious Diseases (DEID), United States Army Medical Research Directorate-Africa (USAMRD-A), Kenya Medical Research Institute (KEMRI)/Walter Reed Project, Kisumu, Kenya
| | - Redempta A. Yeda
- Department of Emerging and Infectious Diseases (DEID), United States Army Medical Research Directorate-Africa (USAMRD-A), Kenya Medical Research Institute (KEMRI)/Walter Reed Project, Kisumu, Kenya
| | - Charles O. Okello
- Department of Emerging and Infectious Diseases (DEID), United States Army Medical Research Directorate-Africa (USAMRD-A), Kenya Medical Research Institute (KEMRI)/Walter Reed Project, Kisumu, Kenya
| | - Jackline A. Juma
- Department of Emerging and Infectious Diseases (DEID), United States Army Medical Research Directorate-Africa (USAMRD-A), Kenya Medical Research Institute (KEMRI)/Walter Reed Project, Kisumu, Kenya
| | - Benjamin H. Opot
- Department of Emerging and Infectious Diseases (DEID), United States Army Medical Research Directorate-Africa (USAMRD-A), Kenya Medical Research Institute (KEMRI)/Walter Reed Project, Kisumu, Kenya
| | - Dennis W. Juma
- Department of Emerging and Infectious Diseases (DEID), United States Army Medical Research Directorate-Africa (USAMRD-A), Kenya Medical Research Institute (KEMRI)/Walter Reed Project, Kisumu, Kenya
| | - Amanda L. Roth
- Department of Emerging and Infectious Diseases (DEID), United States Army Medical Research Directorate-Africa (USAMRD-A), Kenya Medical Research Institute (KEMRI)/Walter Reed Project, Kisumu, Kenya
| | - Hosea M. Akala
- Department of Emerging and Infectious Diseases (DEID), United States Army Medical Research Directorate-Africa (USAMRD-A), Kenya Medical Research Institute (KEMRI)/Walter Reed Project, Kisumu, Kenya
| | - Ben M. Andagalu
- Department of Emerging and Infectious Diseases (DEID), United States Army Medical Research Directorate-Africa (USAMRD-A), Kenya Medical Research Institute (KEMRI)/Walter Reed Project, Kisumu, Kenya
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34
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Hatzade KM, Ghatole AM, Gaidhane PK, Gaidhane MK, Gadekar GP. A facile synthesis of some new pyrimidine-2,4,6-triones analogs and their O-β-D-glucosides P-glycoprotein and antioxidant, antimicrobial study, blood–brain barrier, cytochrome p450 enzyme activity prediction. Med Chem Res 2020. [DOI: 10.1007/s00044-020-02649-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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35
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Padroni G, Patwardhan NN, Schapira M, Hargrove AE. Systematic analysis of the interactions driving small molecule-RNA recognition. RSC Med Chem 2020; 11:802-813. [PMID: 33479676 DOI: 10.1039/d0md00167h] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 05/20/2020] [Indexed: 12/14/2022] Open
Abstract
RNA molecules are becoming an important target class in drug discovery. However, the principles for designing RNA-binding small molecules are yet to be fully uncovered. In this study, we examined the Protein Data Bank (PDB) to highlight privileged interactions underlying small molecule-RNA recognition. By comparing this analysis with previously determined small molecule-protein interactions, we find that RNA recognition is driven mostly by stacking and hydrogen bonding interactions, while protein recognition is instead driven by hydrophobic effects. Furthermore, we analyze patterns of interactions to highlight potential strategies to tune RNA recognition, such as stacking and cation-π interactions that favor purine and guanine recognition, and note an unexpected paucity of backbone interactions, even for cationic ligands. Collectively, this work provides further understanding of RNA-small molecule interactions that may inform the design of small molecules targeting RNA.
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Affiliation(s)
- G Padroni
- Department of Chemistry , Duke University , Durham , North Carolina 27708 , USA .
| | - N N Patwardhan
- Department of Chemistry , Duke University , Durham , North Carolina 27708 , USA .
| | - M Schapira
- Structural Genomics Consortium , University of Toronto , Toronto , ON M5G 1L7 , Canada.,Department of Pharmacology and Toxicology , University of Toronto , Toronto , ON M5S 1A8 , Canada
| | - A E Hargrove
- Department of Chemistry , Duke University , Durham , North Carolina 27708 , USA .
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36
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Janse van Rensburg HD, Legoabe LJ, Terre'Blanche G, Aucamp J. Synthesis and evaluation of methoxy substituted 2-benzoyl-1-benzofuran derivatives as lead compounds for the development adenosine A1 and/or A2A receptor antagonists. Bioorg Chem 2020; 94:103459. [DOI: 10.1016/j.bioorg.2019.103459] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 11/16/2019] [Accepted: 11/19/2019] [Indexed: 12/27/2022]
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37
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In vitro antitumor activity, ADME-Tox and 3D-QSAR of synthesized and selected natural styryl lactones. Comput Biol Chem 2019; 83:107112. [DOI: 10.1016/j.compbiolchem.2019.107112] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 08/13/2019] [Accepted: 08/18/2019] [Indexed: 12/13/2022]
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38
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Raka SC, Ahamed R, Rahman A, Momen AZMR. In silico discovery of noteworthy multi-targeted acetylcholinesterase inhibitors for the treatment of Alzheimer’s disease. ADVANCES IN TRADITIONAL MEDICINE 2019. [DOI: 10.1007/s13596-019-00407-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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39
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Grygorenko OO, Volochnyuk DM, Ryabukhin SV, Judd DB. The Symbiotic Relationship Between Drug Discovery and Organic Chemistry. Chemistry 2019; 26:1196-1237. [PMID: 31429510 DOI: 10.1002/chem.201903232] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 08/19/2019] [Indexed: 12/20/2022]
Abstract
All pharmaceutical products contain organic molecules; the source may be a natural product or a fully synthetic molecule, or a combination of both. Thus, it follows that organic chemistry underpins both existing and upcoming pharmaceutical products. The reverse relationship has also affected organic synthesis, changing its landscape towards increasingly complex targets. This Review article sets out to give a concise appraisal of this symbiotic relationship between organic chemistry and drug discovery, along with a discussion of the design concepts and highlighting key milestones along the journey. In particular, criteria for a high-quality compound library design enabling efficient virtual navigation of chemical space, as well as rise and fall of concepts for its synthetic exploration (such as combinatorial chemistry; diversity-, biology-, lead-, or fragment-oriented syntheses; and DNA-encoded libraries) are critically surveyed.
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Affiliation(s)
- Oleksandr O Grygorenko
- Enamine Ltd., Chervonotkatska Street 78, Kiev, 02094, Ukraine.,Taras Shevchenko National University of Kiev, Volodymyrska Street 60, Kiev, 01601, Ukraine
| | - Dmitriy M Volochnyuk
- Enamine Ltd., Chervonotkatska Street 78, Kiev, 02094, Ukraine.,Taras Shevchenko National University of Kiev, Volodymyrska Street 60, Kiev, 01601, Ukraine.,Institute of Organic Chemistry, National Academy of Sciences of Ukraine, Murmanska Street 5, Kiev, 02660, Ukraine
| | - Sergey V Ryabukhin
- Enamine Ltd., Chervonotkatska Street 78, Kiev, 02094, Ukraine.,Taras Shevchenko National University of Kiev, Volodymyrska Street 60, Kiev, 01601, Ukraine
| | - Duncan B Judd
- Awridian Ltd., Stevenage Bioscience Catalyst, Gunnelswood Road, Stevenage, Herts, SG1 2FX, UK
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40
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Gangarapu NR, Ranganatham A, Reddy EK, Surendra HD, Sajith AM, Yellappa S, Chandrasekhar KB. Design, Synthesis, and Biological Evaluation of 3,5‐Disubstituted 2‐Pyrazineamide Derivatives as Antitubercular Agents. J Heterocycl Chem 2019. [DOI: 10.1002/jhet.3461] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Nagaraja Reddy Gangarapu
- Department of ChemistryGovernment Science College Bengaluru 560001 Karnataka India
- Department of ChemistryJawaharlal Nehru Technological University Ananthapuramu 515002 Andhra Pradesh India
| | - A. Ranganatham
- Laboratory DivisionNational Tuberculosis Institute Bangalore 560003 India
| | - Eeda Koti Reddy
- Division of Chemistry, Department of Science and HumanitiesVignan's Foundation for Science, Technology and Research—VFSTR Vadlamudi Guntur 522213 Andhra Pradesh India
| | - H. D. Surendra
- Laboratory DivisionNational Tuberculosis Institute Bangalore 560003 India
| | - Ayyiliath M. Sajith
- Postgraduate and Research Department of Chemistry, Kasaragod Government CollegeKannur University Kasaragod 671123 Kerala India
| | - Shivaraj Yellappa
- Department of ChemistryGovernment Science College Bengaluru 560001 Karnataka India
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41
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Parulekar RS, Sonawane KD. Molecular modeling studies to explore the binding affinity of virtually screened inhibitor toward different aminoglycoside kinases from diverse MDR strains. J Cell Biochem 2017; 119:2679-2695. [DOI: 10.1002/jcb.26435] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2017] [Accepted: 10/18/2017] [Indexed: 01/17/2023]
Affiliation(s)
| | - Kailas D. Sonawane
- Department of MicrobiologyShivaji UniversityKolhapurMaharashtra (M.S.)India
- Department of Biochemistry, Structural Bioinformatics UnitShivaji UniversityKolhapurMaharashtra (M.S.)India
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42
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DeGoey DA, Chen HJ, Cox PB, Wendt MD. Beyond the Rule of 5: Lessons Learned from AbbVie’s Drugs and Compound Collection. J Med Chem 2017; 61:2636-2651. [DOI: 10.1021/acs.jmedchem.7b00717] [Citation(s) in RCA: 177] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- David A. DeGoey
- Research and Development, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Hui-Ju Chen
- Research and Development, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Philip B. Cox
- Research and Development, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Michael D. Wendt
- Research and Development, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
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43
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Assessing molecular scaffolds for CNS drug discovery. Drug Discov Today 2017; 22:965-969. [DOI: 10.1016/j.drudis.2017.01.008] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 12/04/2016] [Accepted: 01/13/2017] [Indexed: 01/04/2023]
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44
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Daina A, Michielin O, Zoete V. SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Sci Rep 2017; 7:42717. [PMID: 28256516 PMCID: PMC5335600 DOI: 10.1038/srep42717] [Citation(s) in RCA: 6665] [Impact Index Per Article: 952.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 01/13/2017] [Indexed: 02/06/2023] Open
Abstract
To be effective as a drug, a potent molecule must reach its target in the body in sufficient concentration, and stay there in a bioactive form long enough for the expected biologic events to occur. Drug development involves assessment of absorption, distribution, metabolism and excretion (ADME) increasingly earlier in the discovery process, at a stage when considered compounds are numerous but access to the physical samples is limited. In that context, computer models constitute valid alternatives to experiments. Here, we present the new SwissADME web tool that gives free access to a pool of fast yet robust predictive models for physicochemical properties, pharmacokinetics, drug-likeness and medicinal chemistry friendliness, among which in-house proficient methods such as the BOILED-Egg, iLOGP and Bioavailability Radar. Easy efficient input and interpretation are ensured thanks to a user-friendly interface through the login-free website http://www.swissadme.ch. Specialists, but also nonexpert in cheminformatics or computational chemistry can predict rapidly key parameters for a collection of molecules to support their drug discovery endeavours.
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Affiliation(s)
- Antoine Daina
- SIB Swiss Institute of Bioinformatics, Molecular Modeling Group, Quartier Sorge, Bâtiment Génopode, CH-1015 Lausanne, Switzerland
| | - Olivier Michielin
- SIB Swiss Institute of Bioinformatics, Molecular Modeling Group, Quartier Sorge, Bâtiment Génopode, CH-1015 Lausanne, Switzerland.,Department of Oncology, Centre Hospitalier Universitaire Vaudois, CH-1015 Lausanne, Switzerland.,Ludwig Institute for Cancer Research, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Vincent Zoete
- SIB Swiss Institute of Bioinformatics, Molecular Modeling Group, Quartier Sorge, Bâtiment Génopode, CH-1015 Lausanne, Switzerland
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45
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Abdulla O, Clayton AD, Faulkner RA, Gill DM, Rice CR, Walton SM, Sweeney JB. Catalytic sp 3 -sp 3 Functionalisation of Sulfonamides: Late-Stage Modification of Drug-Like Molecules. Chemistry 2017; 23:1494-1497. [PMID: 27897342 DOI: 10.1002/chem.201605464] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Indexed: 12/14/2022]
Abstract
A new application of Pd-catalysed allylation is reported that enables the synthesis of a range of branched sp3 -functionalised sulfonamides, a compound class for which few reported methods exist. By reacting benzyl sulfonamides with allylic acetates in the presence of Pd0 catalysts and base at room temperature, direct allylation was efficiently performed, yielding products that are analogues of structural motifs seen in biologically active small molecules. The reaction was performed under mild conditions and could be applied to nanomolar sigma-receptor binders, thus enabling a late-stage functionalisation and efficient expansion of drug-like chemical space.
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Affiliation(s)
- Othman Abdulla
- Department of Chemical Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK
| | - Adam D Clayton
- Department of Chemical Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK
| | - Robert A Faulkner
- Department of Chemical Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK
| | - Duncan M Gill
- Department of Chemical Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK
| | - Craig R Rice
- Department of Chemical Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK
| | - Scarlett M Walton
- Department of Chemical Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK
| | - Joseph B Sweeney
- Department of Chemical Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK
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46
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Antermite D, Degennaro L, Luisi R. Recent advances in the chemistry of metallated azetidines. Org Biomol Chem 2017; 15:34-50. [DOI: 10.1039/c6ob01665k] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The almost unexplored four-membered azetidines represent a particularly interesting class of molecules, among the family of saturated nitrogen heterocycles. This review reports recent developments in direct metal-based functionalization of the azetidine ring, focusing on the regio- and stereoselectivity of these reactions.
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Affiliation(s)
- Daniele Antermite
- Department of Pharmacy – Drug Sciences
- University of Bari
- Bari 70125
- Italy
| | | | - Renzo Luisi
- Department of Pharmacy – Drug Sciences
- University of Bari
- Bari 70125
- Italy
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47
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Leeson PD. Molecular inflation, attrition and the rule of five. Adv Drug Deliv Rev 2016; 101:22-33. [PMID: 26836397 DOI: 10.1016/j.addr.2016.01.018] [Citation(s) in RCA: 121] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 01/12/2016] [Accepted: 01/18/2016] [Indexed: 12/18/2022]
Abstract
Physicochemical properties underlie all aspects of drug action and are critical for solubility, permeability and successful formulation. Specific physicochemical properties shown to be relevant to oral drugs are size, lipophilicity, ionisation, hydrogen bonding, polarity, aromaticity and shape. The rule of 5 (Ro5) and subsequent studies have raised awareness of the importance of compound quality amongst bioactive molecules. Lipophilicity, probably the most important physical property of oral drugs, has on average changed little over time in oral drugs, until increases in drugs published after 1990. In contrast other molecular properties such as average size have increased significantly. Factors influencing property inflation include the targets pursued, where antivirals frequently violate the Ro5, risk/benefit considerations, and variable drug discovery practices. The compounds published in patents from the pharmaceutical industry are on average larger, more lipophilic and less complex than marketed oral drugs. The variation between individual companies' patented compounds is due to different practices and not to the targets pursued. Overall, there is demonstrable physical property attrition in moving from patents to candidate drugs to marketed drugs. The pharmaceutical industry's recent poor productivity has been due, in part, to progression of molecules that are unable to unambiguously test clinical efficacy, and attrition can therefore be improved by ensuring candidate drug quality is 'fit for purpose.' The combined ligand efficiency (LE) and lipophilic ligand efficiency (LLE) values of many marketed drugs are optimised relative to other molecules acting at the same target. Application of LLE in optimisation can help identify improved leads, even with challenging targets that seem to require lipophilic ligands. Because of their targets, some projects may need to pursue 'beyond Ro5' physicochemical space; such projects will require non-standard lead generation and optimisation and should not dominate in a well-balanced portfolio. Compound quality is controllable by lead selection and optimisation and should not be a cause of clinical failure.
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Affiliation(s)
- Paul D Leeson
- Paul Leeson Consulting Ltd, The Malt House, Main Street, Congerstone, Nuneaton, Warks CV13 6LZ, UK.
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48
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Meanwell NA. Improving Drug Design: An Update on Recent Applications of Efficiency Metrics, Strategies for Replacing Problematic Elements, and Compounds in Nontraditional Drug Space. Chem Res Toxicol 2016; 29:564-616. [DOI: 10.1021/acs.chemrestox.6b00043] [Citation(s) in RCA: 120] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nicholas A. Meanwell
- Department of Discovery Chemistry, Bristol-Myers Squibb Research & Development, Wallingford, Connecticut 06492, United States
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49
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Affron DP, Bull JA. Palladium-Catalyzed Directed C(sp 3)-H Arylation of Saturated Heterocycles at C-3 Using a Concise Optimization Approach. European J Org Chem 2016; 2016:139-149. [PMID: 26877706 PMCID: PMC4736452 DOI: 10.1002/ejoc.201501300] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Indexed: 11/18/2022]
Abstract
Saturated heterocycles, such as THFs, pyrrolidines, piperidines and THPs, are essential components of many biologically active compounds. Examples of C-H functionalization on these important ring systems remain scarce, especially at unactivated positions. Here we report the development of conditions for the palladium-catalyzed stereoselective C(sp3)-H arylation at unactivated 3-positions of 5- and 6-membered N- and O-heterocycles with aminoquinoline directing groups. Subtle differences in substrate structures altered their reactivity significantly; and different conditions were required to achieve high yields in each case. Successful conditions were developed using a short empirical optimization approach to cover reaction space with a limited set of variables. Excellent cis-selectivity was achieved in all cases, except for the THP substrate where minor trans-products were formed through a different palladacyclic intermediate. Here, differences in reactivity and selectivity with other directing groups were examined.
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Affiliation(s)
- Dominic P. Affron
- Department of Chemistry, Imperial College London, South Kensington, London SW7 2AZ, United Kingdom, http://www3.imperial.ac.uk/people/j.bull
| | - James A. Bull
- Department of Chemistry, Imperial College London, South Kensington, London SW7 2AZ, United Kingdom, http://www3.imperial.ac.uk/people/j.bull
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50
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Degennaro L, Carroccia L, Parisi G, Zenzola M, Romanazzi G, Fanelli F, Pisano L, Luisi R. Regio- and Stereoselective Synthesis of Sulfur-Bearing Four-Membered Heterocycles: Direct Access to 2,4-Disubstituted Thietane 1-Oxides. J Org Chem 2015; 80:12201-11. [DOI: 10.1021/acs.joc.5b02126] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Leonardo Degennaro
- Department
of Pharmacy − Drug Sciences, University of Bari “A. Moro”, Via E. Orabona 4, 70125 Bari, Italy
| | - Laura Carroccia
- Department
of Pharmacy − Drug Sciences, University of Bari “A. Moro”, Via E. Orabona 4, 70125 Bari, Italy
| | - Giovanna Parisi
- Department
of Pharmacy − Drug Sciences, University of Bari “A. Moro”, Via E. Orabona 4, 70125 Bari, Italy
| | - Marina Zenzola
- Department
of Pharmacy − Drug Sciences, University of Bari “A. Moro”, Via E. Orabona 4, 70125 Bari, Italy
| | - Giuseppe Romanazzi
- DICATECh, Politecnico di Bari, Via Orabona 4, 70125 Bari, Italy
- CNR NANOTEC−Istituto di Nanotecnologia, Polo di Nanotecnologia c/o Campus Ecotekne, via
Monteroni, 73100 Lecce, Italy
| | - Flavio Fanelli
- Department
of Pharmacy − Drug Sciences, University of Bari “A. Moro”, Via E. Orabona 4, 70125 Bari, Italy
- CNR, Institute of Crystallography IC-CNR, Amendola, 122/o, 70125 Bari, Italy
| | - Luisa Pisano
- Department
of Chemistry and Pharmacy, University of Sassari, Via Vienna 2, 07100 Sassari, Italy
| | - Renzo Luisi
- Department
of Pharmacy − Drug Sciences, University of Bari “A. Moro”, Via E. Orabona 4, 70125 Bari, Italy
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