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Arif B, Yasir S, Saeed M, Fatmi MQ. Natural products can be potential inhibitors of metalloproteinase II from Bacteroides fragilis to intervene colorectal cancer. Heliyon 2024; 10:e32838. [PMID: 39005891 PMCID: PMC11239599 DOI: 10.1016/j.heliyon.2024.e32838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 05/03/2024] [Accepted: 06/10/2024] [Indexed: 07/16/2024] Open
Abstract
Bacteroides fragilis, a gram negative and obligate anaerobe bacterium, is a member of normal gut microbiota and facilitates many essential roles being performed in human body in normal circumstances specifically in Gastrointestinal or GI tract. Sometimes, due to genetics, epigenetics, and environmental factors, Bacteroides fragilis and their protein(s) start interacting with intestinal epithelium thus damaging the lining leading to colorectal cancers (CRC). To identify these protein(s), we incorporated a novel subtractive proteomics approach in the study. Metalloproteinase II (MPII), a Bacteroides fragilis toxin (bft), was investigated for its virulence and unique pathways to demonstrate its specificity and uniqueness in pathogenicity followed by molecular docking against a set of small drug-like natural molecules to discover potential inhibitors against the toxin. All these identified inhibitor-like molecules were analyzed for their ADMET calculations and detailed physiochemical properties to predict their druggability, GI absorption, blood brain barrier and skin permeation, and others. Resultantly, a total of ten compounds with the least binding energies were obtained and were subjected to protein-compound interaction analysis. Interaction analysis revealed the most common ligand-interacting residues in MPII are His 345, Glu 346, His 339, Gly 310, Tyr 341, Pro 340, Asp 187, Phe 309, Lys 307, Ile 185, Thr 308, and Pro 184. Therefore, top three compounds complexed with MPII having best binding energies were selected in order to analyze their trajectories. RMSD, RMSF, Rg and MMPBSA analysis revealed that all compounds showed good binding and keeping the complex stable and compact throughout the simulation time in addition to all properties and qualities of being a potential inhibitor against MPII.
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Affiliation(s)
- Bushra Arif
- Department of Biosciences, COMSATS University Islamabad, Islamabad Campus, Pakistan
| | - Saba Yasir
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Muhammad Saeed
- Department of Biosciences, COMSATS University Islamabad, Islamabad Campus, Pakistan
| | - M. Qaiser Fatmi
- Department of Biosciences, COMSATS University Islamabad, Islamabad Campus, Pakistan
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2
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Sarfraz M, Ayyaz M, Rauf A, Yaqoob A, Tooba, Arif Ali M, Siddique SA, Qureshi AM, Sarfraz MH, Aljowaie RM, Almutairi SM, Arshad M. New Pyrimidinone Bearing Aminomethylenes and Schiff Bases as Potent Antioxidant, Antibacterial, SARS-CoV-2, and COVID-19 Main Protease M Pro Inhibitors: Design, Synthesis, Bioactivities, and Computational Studies. ACS OMEGA 2024; 9:25730-25747. [PMID: 38911743 PMCID: PMC11191110 DOI: 10.1021/acsomega.3c09393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 05/18/2024] [Accepted: 05/23/2024] [Indexed: 06/25/2024]
Abstract
New 2-thioxopyrimidinone derivatives (A1-A10) were synthesized in 87-96% yields via a simple three-component condensation reaction. These compounds were screened extensively through in vitro assays for antioxidant and antibacterial investigations. The DPPH assays resulted in the excellent potency of A6-A10 as antioxidants with IC50 values of 0.83 ± 0.125, 0.90 ± 0.77, 0.36 ± 0.063, 1.4 ± 0.07, and 1.18 ± 0.06 mg/mL, which were much better than 1.79 ± 0.045 mg/mL for the reference ascorbic acid. These compounds exhibited better antibacterial potency against Klebsiella with IC50 values of 2 ± 7, 1.32 ± 8.9, 1.19 ± 11, 1.1 ± 12, and 1.16 ± 11 mg/mL for A6-A10. High-throughput screenings (HTS) of these motifs were carried out including investigation of drug-like behaviors, physiochemical property evaluation, and structure-related studies involving DFT and metabolic transformation trends. The radical scavenging ability of the synthesized motifs was validated through molecular docking studies through ligand-protein binding against human inducible nitric oxide synthase (HINOS) PDB ID: 4NOS, and the results were promising. Furthermore, the antiviral capability of the compounds was examined by in silico studies using two viral proteins PDB ID: 6Y84 and PDB ID: 6LU7. Binding poses of ligands were discussed, and amino acids in the protein binding pockets were investigated, where the tested compounds showed much better binding affinities than the standard inhibitors, proving to be suitable leads for antiviral drug discovery. The stabilities of the molecular docked complexes in real systems were validated by molecular dynamics simulations.
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Affiliation(s)
- Muhammad Sarfraz
- Institute
of Chemistry, The Islamia University of
Bahawalpur, Bahawalpur 63100, Pakistan
| | - Muhammad Ayyaz
- Institute
of Chemistry, The Islamia University of
Bahawalpur, Bahawalpur 63100, Pakistan
| | - Abdul Rauf
- Institute
of Chemistry, The Islamia University of
Bahawalpur, Bahawalpur 63100, Pakistan
| | - Asma Yaqoob
- Institute
of Biochemistry, Biotechnology, and Bioinformatics. Department of
Biochemistry and Molecular Biology, The
Islamia University of Bahawalpur, Bahawalpur 63100, Pakistan
| | - Tooba
- Institute
of Biochemistry, Biotechnology, and Bioinformatics. Department of
Biochemistry and Molecular Biology, The
Islamia University of Bahawalpur, Bahawalpur 63100, Pakistan
| | - Muhammad Arif Ali
- Institute
of Chemistry, The Islamia University of
Bahawalpur, Bahawalpur 63100, Pakistan
| | - Sabir Ali Siddique
- Institute
of Chemistry, The Islamia University of
Bahawalpur, Bahawalpur 63100, Pakistan
| | - Ashfaq Mahmood Qureshi
- Department
of Chemistry, Government Sadiq College Women
University, Bahawalpur 63100, Pakistan
| | - Muhammad Hassan Sarfraz
- Nuffield
Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences,
Botnar Institute of Musculoskeletal Sciences, University of Oxford, OxfordOX3 7LD, United
Kingdom
| | - Reem M. Aljowaie
- Department
of Botany and Microbiology, College of Science, King Saud University, P O 2455 Riyadh 11451, Saudi Arabia
| | - Saeedah Musaed Almutairi
- Department
of Botany and Microbiology, College of Science, King Saud University, P O 2455 Riyadh 11451, Saudi Arabia
| | - Muhammad Arshad
- Institute
of Chemistry, The Islamia University of
Bahawalpur, Bahawalpur 63100, Pakistan
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3
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Elrashedy A, Nayel M, Salama A, Salama MM, Hasan ME. Bioinformatics approach for structure modeling, vaccine design, and molecular docking of Brucella candidate proteins BvrR, OMP25, and OMP31. Sci Rep 2024; 14:11951. [PMID: 38789443 PMCID: PMC11126717 DOI: 10.1038/s41598-024-61991-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 05/13/2024] [Indexed: 05/26/2024] Open
Abstract
Brucellosis is a zoonotic disease with significant economic and healthcare costs. Despite the eradication efforts, the disease persists. Vaccines prevent disease in animals while antibiotics cure humans with limitations. This study aims to design vaccines and drugs for brucellosis in animals and humans, using protein modeling, epitope prediction, and molecular docking of the target proteins (BvrR, OMP25, and OMP31). Tertiary structure models of three target proteins were constructed and assessed using RMSD, TM-score, C-score, Z-score, and ERRAT. The best models selected from AlphaFold and I-TASSER due to their superior performance according to CASP 12 - CASP 15 were chosen for further analysis. The motif analysis of best models using MotifFinder revealed two, five, and five protein binding motifs, however, the Motif Scan identified seven, six, and eight Post-Translational Modification sites (PTMs) in the BvrR, OMP25, and OMP31 proteins, respectively. Dominant B cell epitopes were predicted at (44-63, 85-93, 126-137, 193-205, and 208-237), (26-46, 52-71, 98-114, 142-155, and 183-200), and (29-45, 58-82, 119-142, 177-198, and 222-251) for the three target proteins. Additionally, cytotoxic T lymphocyte epitopes were detected at (173-181, 189-197, and 202-210), (61-69, 91-99, 159-167, and 181-189), and (3-11, 24-32, 167-175, and 216-224), while T helper lymphocyte epitopes were displayed at (39-53, 57-65, 150-158, 163-171), (79-87, 95-108, 115-123, 128-142, and 189-197), and (39-47, 109-123, 216-224, and 245-253), for the respective target protein. Furthermore, structure-based virtual screening of the ZINC and DrugBank databases using the docking MOE program was followed by ADMET analysis. The best five compounds of the ZINC database revealed docking scores ranged from (- 16.8744 to - 15.1922), (- 16.0424 to - 14.1645), and (- 14.7566 to - 13.3222) for the BvrR, OMP25, and OMP31, respectively. These compounds had good ADMET parameters and no cytotoxicity, while DrugBank compounds didn't meet Lipinski's rule criteria. Therefore, the five selected compounds from the ZINC20 databases may fulfill the pharmacokinetics and could be considered lead molecules for potentially inhibiting Brucella's proteins.
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Affiliation(s)
- Alyaa Elrashedy
- Department of Animal Medicine and Infectious Diseases (Infectious Diseases), Faculty of Veterinary Medicine, University of Sadat City, Sadat City, Egypt.
| | - Mohamed Nayel
- Department of Animal Medicine and Infectious Diseases (Infectious Diseases), Faculty of Veterinary Medicine, University of Sadat City, Sadat City, Egypt
| | - Akram Salama
- Department of Animal Medicine and Infectious Diseases (Infectious Diseases), Faculty of Veterinary Medicine, University of Sadat City, Sadat City, Egypt
| | - Mohammed M Salama
- Physics Department, Medical Biophysics Division, Faculty of Science, Helwan University, Cairo, Egypt
| | - Mohamed E Hasan
- Bioinformatics Department, Genetic Engineering and Biotechnology Research Institute, University of Sadat City, Sadat City, Egypt
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Nkungli NK, Fouegue ADT, Tasheh SN, Bine FK, Hassan AU, Ghogomu JN. In silico investigation of falcipain-2 inhibition by hybrid benzimidazole-thiosemicarbazone antiplasmodial agents: A molecular docking, molecular dynamics simulation, and kinetics study. Mol Divers 2024; 28:475-496. [PMID: 36622482 PMCID: PMC9838286 DOI: 10.1007/s11030-022-10594-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 12/20/2022] [Indexed: 01/10/2023]
Abstract
The emergence of artemisinin-resistant variants of Plasmodium falciparum necessitates the urgent search for novel antimalarial drugs. In this regard, an in silico study to screen antimalarial drug candidates from a series of benzimidazole-thiosemicarbazone hybrid molecules with interesting antiplasmodial properties and explore their falcipain-2 (FP2) inhibitory potentials has been undertaken herein. FP2 is a key cysteine protease that degrades hemoglobin in Plasmodium falciparum and is an important biomolecular target in the development of antimalarial drugs. Pharmacokinetic properties, ADMET profiles, MM/GBSA-based binding free energies, reaction mechanisms, and associated barrier heights have been investigated. DFT, molecular dynamics simulation, molecular docking, and ONIOM methods were used. From the results obtained, four 4N-substituted derivatives of the hybrid molecule (E)-2-(1-(5-chloro-1H-benzo[d]imidazol-2-yl)ethylidene)hydrazine-1-carbothioamide (1A) denoted 1B, 1C, 1D, and 1E are drug-like and promising inhibitors of FP2, exhibiting remarkably small inhibitory constants (5.94 × 10-14 - 2.59 × 10-04 n M) and favorable binding free energies (-30.32 to -17.17 kcal/mol). Moreover, the ONIOM results have revealed that 1B and possibly 1C and 1D may act as covalent inhibitors of FP2. The rate-determining step of the thermodynamically favorable covalent binding mechanism occurs across a surmountable barrier height of 24.18 kcal/mol in water and 28.42 kcal/mol in diethyl ether. Our findings are useful for further experimental investigations on the antimalarial activities of the hybrid molecules studied.
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Affiliation(s)
- Nyiang Kennet Nkungli
- Department of Chemistry, Faculty of Science, The University of Bamenda, Bambili, P. O. Box 39, Bamenda, Cameroon.
| | - Aymard Didier Tamafo Fouegue
- Department of Chemistry, Higher Teacher Training College Bertoua, University of Bertoua, P.O. Box 652, Bertoua, Cameroon
| | - Stanley Numbonui Tasheh
- Department of Chemistry, Faculty of Science, The University of Bamenda, Bambili, P. O. Box 39, Bamenda, Cameroon
- Department of Chemistry, Faculty of Science, University of Dschang, P. O. Box 67, Dschang, Cameroon
| | - Fritzgerald Kogge Bine
- Department of Chemistry, Faculty of Science, University of Dschang, P. O. Box 67, Dschang, Cameroon
| | - Abrar Ul Hassan
- Department of Chemistry, University of Gujrat, Gujrat, 54400, PK, Pakistan
| | - Julius Numbonui Ghogomu
- Department of Chemistry, Faculty of Science, The University of Bamenda, Bambili, P. O. Box 39, Bamenda, Cameroon
- Department of Chemistry, Faculty of Science, University of Dschang, P. O. Box 67, Dschang, Cameroon
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Oluwafemi KA, Oyeneyin OE, Babatunde DD, Agbaffa EB, Aigbogun JA, Odeja OO, Emmanuel AV. Parasitic Protozoans: Exploring the Potential of N,N'-Bis[2-(5-bromo-7-azabenzimidazol-1-yl)-2-oxoethyl]ethylene-1,3-Diamine and Its Cyclohexyl-1,2-diamine Analogue as TryR and Pf-DHODH Inhibitors. Acta Parasitol 2023; 68:807-819. [PMID: 37821729 DOI: 10.1007/s11686-023-00719-5] [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: 06/17/2022] [Accepted: 08/26/2023] [Indexed: 10/13/2023]
Abstract
PURPOSE Major human parasitic protozoans, such as Plasmodium falciparum and Trypanosoma brucei, cause malaria and trypanosomiasis also known as sleeping sickness. In anti-parasitic drug discovery research, trypanothione reductase (TryR) and P. falciparum dihydroorotate dehydrogenase (Pf-DHODH) enzymes are key drug targets in T. brucei and P. falciparum, respectively. The possibility of co-infection of single host by T. brucei and P. falciparum is because both parasites exist in sub-Saharan Africa and the problem of parasite drug resistance necessitates the discovery of new scaffolds, which are strange to the organisms causing these infectious diseases-new scaffolds may help overcome established resistance mechanisms of the organisms. METHOD In this study, N,N'-bis[2-(5-bromo-7-azabenzimidazol-1-yl)-2-oxoethyl]ethylene-1,3-diamine and its cyclohexyl-1,2-diamine analogue were explored for their inhibitory potential against TryR and Pf-DHODH by engaging density functional study, molecular dynamic simulations, drug-likeness, in silico and in vitro studies RESULTS/CONCLUSION: Results obtained indicated excellent binding potential of the ligands to the receptors and good ADMET (adsorption, desorption, metabolism, excretion, and toxicity) properties.
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Affiliation(s)
- Kola A Oluwafemi
- Department of Chemical Sciences, Adekunle Ajasin University, Akungba-Akoko, Nigeria.
| | - Oluwatoba E Oyeneyin
- Department of Chemical Sciences, Adekunle Ajasin University, Akungba-Akoko, Nigeria.
- Theoretical and Computational Chemistry Unit, Adekunle Ajasin University, Akungba-Akoko, Nigeria.
| | | | - Eric B Agbaffa
- Department of Chemistry, Federal University of Technology, Akure, Nigeria
- Department of Physical Sciences, Wesley University, Ondo, Nigeria
| | - Jane A Aigbogun
- Department of Chemistry, Federal University of Technology, Akure, Nigeria
| | - Oluwakayode O Odeja
- Department of Chemistry, Federal University of Petroleum Recourses, Effurun, Nigeria
| | - Abiodun V Emmanuel
- Department of Chemical Sciences, Adekunle Ajasin University, Akungba-Akoko, Nigeria
- Theoretical and Computational Chemistry Unit, Adekunle Ajasin University, Akungba-Akoko, Nigeria
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6
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Olaokun OO, Zubair MS. Antidiabetic Activity, Molecular Docking, and ADMET Properties of Compounds Isolated from Bioactive Ethyl Acetate Fraction of Ficus lutea Leaf Extract. Molecules 2023; 28:7717. [PMID: 38067448 PMCID: PMC10708125 DOI: 10.3390/molecules28237717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/17/2023] [Accepted: 11/20/2023] [Indexed: 12/18/2023] Open
Abstract
Diabetes contributes to the rising global death rate. Despite scientific advancements in understanding and managing diabetes, no single therapeutic agent has been identified to effectively treat and prevent its progression. Consequently, the exploration for new antidiabetic therapeutics continues. This study aimed to investigate the antidiabetic bioactive ethyl acetate fraction of F. lutea at the molecular level to understand the molecular interactions and ligand-protein binding. To do this, the fraction underwent column chromatography fractionation to yield five compounds: lupeol, stigmasterol, α-amyrin acetate, epicatechin, and epiafzelechin. These compounds were evaluated in vitro through α-glucosidase inhibition and glucose utilization assays in C2C12 muscle and H-4-11-E liver cells using standard methods. In silico analysis was conducted using molecular docking and ADMET studies. Epicatechin exhibited the most potent α-glucosidase inhibition (IC50 = 5.72 ± 2.7 µg/mL), while epiafzelechin stimulated superior glucose utilization in C2C12 muscle cells (33.35 ± 1.8%) and H-4-11-E liver cells (46.7 ± 1.2%) at a concentration of 250 µg/mL. The binding energies of the isolated compounds for glycogen phosphorylase (1NOI) and α-amylase (1OSE) were stronger (<-8.1) than those of the positive controls. Overall, all tested compounds exhibited characteristics indicative of their potential as antidiabetic agents; however, toxicity profiling predicted epiafzelechin and epicatechin as better alternatives. The ethyl acetate fraction and its compounds, particularly epiafzelechin, showed promise as antidiabetic agents. However, further comprehensive studies are necessary to validate these findings.
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Affiliation(s)
- Oyinlola O. Olaokun
- Department of Biology and Environmental Science, School of Science and Technology, Sefako Makgatho Health Science University, Molotlegi Street, Ga-Rankuwa, Pretoria 0204, South Africa
| | - Muhammad S. Zubair
- Natural Product Research Group, Department of Pharmacy, Faculty of Science, Tadulako University, Palu-Central Sulawesi 94118, Indonesia;
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Oselusi SO, Sibuyi NRS, Meyer M, Madiehe AM. Ehretia Species Phytoconstituents as Potential Lead Compounds against Klebsiella pneumoniae Carbapenemase: A Computational Approach. BIOMED RESEARCH INTERNATIONAL 2023; 2023:8022356. [PMID: 37869630 PMCID: PMC10586912 DOI: 10.1155/2023/8022356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 09/05/2023] [Accepted: 09/26/2023] [Indexed: 10/24/2023]
Abstract
The evolution of antibiotic-resistant carbapenemase has negatively impacted the management of critical healthcare-associated infections. K. pneumoniae carbapenemase-2- (KPC-2-) expressing bacteria have developed resistance to conventional therapeutic options, including those used as a last resort for life-threatening diseases. In this study, Ehretia species phytoconstituents were screened for their potential to inhibit KPC-2 protein using in silico approaches. Molecular docking was used to identify strong KPC-2 protein binding phytoconstituents retrieved from the literature. The best-docked conformation of the ligands was selected based on their glide energy and binding interactions. To determine their binding free energies, these hit compounds were subjected to molecular mechanics with generalized born and surface area (MM-GBSA) in the PRIME module. Pharmacological assessments of the ligands were performed to evaluate their drug-likeness. Molecular dynamic (MD) simulations were used to analyze the conformational stability of the selected druglike compounds within the active site of the KPC-2 protein. Overall, a total of 69 phytoconstituents were compiled from the literature. Fourteen of these compounds exhibited a stronger binding affinity for the protein target than the reference drugs. Four of these top hit compounds, DB09, DB12, DB28, and DB66, revealed the highest efficacy in terms of drug-likeness properties. The MD simulation established that among the druglike compounds, DB66 attained stable conformations after 150 ns simulation in the active site of the protein. We concluded that DB66 from Ehretia species could play a significant role in therapeutic efforts against KPC-2-expressing bacteria.
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Affiliation(s)
- Samson O. Oselusi
- Nanobiotechnology Research Group, Department of Biotechnology, University of the Western Cape, Private Bag X17, Bellville, Cape Town 7535, South Africa
- DSI/Mintek Nanotechnology Innovation Centre (NIC), Biolabels Research Node, Department of Biotechnology, University of the Western Cape, Private Bag X17, Bellville, Cape Town 7535, South Africa
| | - Nicole R. S. Sibuyi
- DSI/Mintek Nanotechnology Innovation Centre (NIC), Biolabels Research Node, Department of Biotechnology, University of the Western Cape, Private Bag X17, Bellville, Cape Town 7535, South Africa
| | - Mervin Meyer
- DSI/Mintek Nanotechnology Innovation Centre (NIC), Biolabels Research Node, Department of Biotechnology, University of the Western Cape, Private Bag X17, Bellville, Cape Town 7535, South Africa
| | - Abram M. Madiehe
- Nanobiotechnology Research Group, Department of Biotechnology, University of the Western Cape, Private Bag X17, Bellville, Cape Town 7535, South Africa
- DSI/Mintek Nanotechnology Innovation Centre (NIC), Biolabels Research Node, Department of Biotechnology, University of the Western Cape, Private Bag X17, Bellville, Cape Town 7535, South Africa
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Adewumi AT, Oluyemi WM, Adekunle YA, Adewumi N, Alahmdi MI, Soliman MES, Abo‐Dya NE. Propitious Indazole Compounds as β‐ketoacyl‐ACP Synthase Inhibitors and Mechanisms Unfolded for TB Cure: Integrated Rational Design and MD Simulations. ChemistrySelect 2023. [DOI: 10.1002/slct.202203877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Adeniyi T. Adewumi
- Molecular Bio-computation and Drug Design Laboratory School of Health Sciences University of KwaZulu-Natal Westville Campus Durban 4001 South Africa
- Research Laboratories for Rational Design of Drugs and Biomaterials Isiphephelo Court, Tsakane 1550 Brakpan, Johannesburg East Rand Gauteng South Africa
| | - Wande M. Oluyemi
- Research Laboratories for Rational Design of Drugs and Biomaterials Isiphephelo Court, Tsakane 1550 Brakpan, Johannesburg East Rand Gauteng South Africa
- Department of Pharmaceutical and Medicinal Chemistry College of Pharmacy Afe Babalola University Ado-Ekiti Ekiti State Nigeria
- Laboratory for Natural Products and Biodiscovery Research Pharmaceutical Chemistry Department Faculty of Pharmacy University of Ibadan Nigeria
| | - Yemi A. Adekunle
- Research Laboratories for Rational Design of Drugs and Biomaterials Isiphephelo Court, Tsakane 1550 Brakpan, Johannesburg East Rand Gauteng South Africa
- Laboratory for Natural Products and Biodiscovery Research Pharmaceutical Chemistry Department Faculty of Pharmacy University of Ibadan Nigeria
- Centre for Natural Products Discovery (CNPD) School of Pharmacy and Biomolecular Sciences Liverpool John Moores University Liverpool L3 3AF United Kingdom
| | - Nonhlanhla Adewumi
- Research Laboratories for Rational Design of Drugs and Biomaterials Isiphephelo Court, Tsakane 1550 Brakpan, Johannesburg East Rand Gauteng South Africa
- Department of Chemistry Faculty of Applied and Computer Sciences Vaal University Vanderbijl Park South Africa
- Chemical research Laboratory BetaChem Pty Ltd ERF5 Producta Road, Driemanskap, Heidelberg 1441 Gauteng South Africa
| | - Mohamed Issa Alahmdi
- Department of Chemistry Faculty of Science University of Tabuk, Tabuk, 7149 Saudi Arabia
| | - Mahmoud E. S. Soliman
- Molecular Bio-computation and Drug Design Laboratory School of Health Sciences University of KwaZulu-Natal Westville Campus Durban 4001 South Africa
| | - Nader E. Abo‐Dya
- Department of Pharmaceutical Chemistry Faculty of Pharmacy Tabuk University Tabuk 71491 Saudi Arabia
- Department of Pharmaceutical Organic Chemistry Faculty of Pharmacy Zagazig University Zagazig 44519 Egypt
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Ma E, Jin L, Qian C, Feng C, Zhao Z, Tian H, Yang D. Bioinformatics-Guided Identification of Ethyl Acetate Extract of Citri Reticulatae Pericarpium as a Functional Food Ingredient with Anti-Inflammatory Potential. Molecules 2022; 27:molecules27175435. [PMID: 36080202 PMCID: PMC9457579 DOI: 10.3390/molecules27175435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 08/18/2022] [Accepted: 08/22/2022] [Indexed: 11/23/2022] Open
Abstract
Citri Reticulatae Pericarpium (CRP) is one of the most commonly used food supplements and folk medicines worldwide, and possesses cardiovascular, digestive, and respiratory protective effects partially through its antioxidant and anti-inflammatory functions. The unique aromatic flavor and mild side effects make CRP a promising candidate for the development of anti-inflammatory functional food. However, recent studies show that the crude alcoholic extract and some isolated compounds of CRP show compromised anti-inflammatory activity, which became the main factor hindering its further development. To identify the bioactive compounds with anti-inflammatory potential, and improve the anti-inflammatory effects of the extract, a bioinformatics-guided extraction protocol was employed in this study. The potential bioactive candidates were identified by combing network pharmacology analysis, molecular docking, principal components analysis, k-means clustering, and in vitro testing of reference compounds. Our results demonstrated that 66 compounds in CRP could be grouped into four clusters according to their docking score profile against 24 receptors, while the cluster containing flavonoids and phenols might possess a more promising anti-inflammatory function. In addition, in vitro anti-inflammatory tests of the seven reference compounds demonstrated that hesperitin, naringenin, and gardenin B, which were grouped into a cluster containing flavonoids and phenols, significantly decreased LPS-induced NO, TNF-α, and IL-6 production of macrophages. While the compounds outside of that cluster, such as neohesperidin, naringin, hesperidin, and sinensetin showed little effect on alleviating LPS-induced NO and proinflammatory cytokine production. Based on the chemical properties of selected compounds, ethyl acetate (EtOAc) was selected as the solvent for extraction, because of its promising solubility of flavonoids and phenols. Furthermore, the ethanol alcoholic extract was used as a reference. The chemical profiling of EtOAc and crude alcoholic extract by HPLC/MS/MS also demonstrated the decreased abundance of flavonoid glycosides in EtOAc extract but increased abundance of phenols, phenolic acid, and aglycones. In accordance with the prediction, the EtOAc extract of CRP, but not the crude alcoholic extract, significantly decreased the NO, IL-6, and TNF-α production. Taken together, the results suggested selective extraction of phenols and flavonoids rich extract was able to increase the anti-inflammatory potential of CRP partially because of the synergistic effects between flavonoids, phenols, and enriched polymethoxyflavones. Our study might pave the road for the development of ethyl acetate extract of CRP as a novel functional food with anti-inflammatory function.
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Affiliation(s)
- Enyao Ma
- Guangdong Hanchao Traditional Chinese Medicine Technology Co., Ltd., Guangzhou 510163, China
| | - Lu Jin
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
- Correspondence:
| | - Chunguo Qian
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Chong Feng
- Guangzhou Caizhilin Pharmaceutical Co., Ltd., Guangzhou 510360, China
| | - Zhimin Zhao
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Hongru Tian
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Depo Yang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
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Ouyang Y, Huang JJ, Wang YL, Zhong H, Song BA, Hao GF. In Silico Resources of Drug-Likeness as a Mirror: What Are We Lacking in Pesticide-Likeness? JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:10761-10773. [PMID: 34516106 DOI: 10.1021/acs.jafc.1c01460] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Unfavorable bioavailability is an important aspect underlying the failure of drug candidates. Computational approaches for evaluating drug-likeness can minimize these risks. Over the past decades, computational approaches for evaluating drug-likeness have sped up the process of drug development and were also quickly derived to pesticide-likeness. As a result of many critical differences between drugs and pesticides, many kinds of methods for drug-likeness cannot be used for pesticide-likeness. Therefore, it is crucial to comprehensively compare and analyze the differences between drug-likeness and pesticide-likeness, which may provide a basis for solving the problems encountered during the evaluation of pesticide-likeness. Here, we systematically collected the recent advances of drug-likeness and pesticide-likeness and compared their characteristics. We also evaluated the current lack of studies on pesticide-likeness, the molecular descriptors and parameters adopted, the pesticide-likeness model on pesticide target organisms, and comprehensive analysis tools. This work may guide researchers to use appropriate methods for developing pesticide-likeness models. It may also aid non-specialists to understand some important concepts in drug-likeness and pesticide-likeness.
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Affiliation(s)
- Yan Ouyang
- Guizhou Engineering Laboratory for Synthetic Drugs, Key Laboratory of Guizhou Fermentation Engineering and Biomedicine, School of Pharmaceutical Sciences, Guizhou University, Guiyang, Guizhou 550025, People's Republic of China
| | - Jun-Jie Huang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Research and Development Center for Fine Chemicals, Guizhou University, Guiyang, Guizhou 550025, People's Republic of China
| | - Yu-Liang Wang
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, Hubei 430079, People's Republic of China
- International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan, Hubei 430079, People's Republic of China
| | - Hang Zhong
- Guizhou Engineering Laboratory for Synthetic Drugs, Key Laboratory of Guizhou Fermentation Engineering and Biomedicine, School of Pharmaceutical Sciences, Guizhou University, Guiyang, Guizhou 550025, People's Republic of China
| | - Bao-An Song
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Research and Development Center for Fine Chemicals, Guizhou University, Guiyang, Guizhou 550025, People's Republic of China
| | - Ge-Fei Hao
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Research and Development Center for Fine Chemicals, Guizhou University, Guiyang, Guizhou 550025, People's Republic of China
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Ibrahim ZY, Uzairu A, Shallangwa GA, Abechi SE. Pharmacokinetic predictions and docking studies of substituted aryl amine-based triazolopyrimidine designed inhibitors of Plasmodium falciparum dihydroorotate dehydrogenase (PfDHODH). FUTURE JOURNAL OF PHARMACEUTICAL SCIENCES 2021. [DOI: 10.1186/s43094-021-00288-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
The sixteen (16) designed data set of substituted aryl amine-based triazolopyrimidine were docked against Plasmodium falciparum dihydroorotate dehydrogenase (PfDHODH) employing Molegro Virtual Docker (MVD) software and their pharmacokinetic property determined through SwissADME predictor.
Results
The docking studies shows compound D16, 5-((6-methoxy-5-methyl-[1,2,4]triazolo[1,5-a]pyrimidin-7-yl)amino)benzo[b]thiophen-4-ol to be the most interactive and stable derivative (re-rank score = − 114.205 kcal/mol) resulting from the hydrophobic as well as hydrogen interactions. The hydrogen interaction produced one hydrogen bond with the active residues LEU359 (H∙∙H∙∙O) at a bond distances of 2.2874 Å. All the designed derivatives were found to pass the Lipinski rule of five tests, supporting the drug-likeliness of the designed compounds.
Conclusion
The ADME analysis revealed a perfect concurrence with the Lipinski Ro5, where the derivatives were found to possess good pharmacokinetic properties such as molar refractivity (MR), number of rotatable bonds (nRotb), log of skin permeability (log Kp), blood-brain barrier (BBB). These results could a deciding factor for the optimization of novel antimalarial compounds.
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