1
|
Santangelo BE, Bada M, Hunter LE, Lozupone C. Hypothesizing mechanistic links between microbes and disease using knowledge graphs. Sci Rep 2025; 15:6905. [PMID: 40011529 PMCID: PMC11865272 DOI: 10.1038/s41598-025-91230-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2024] [Accepted: 02/19/2025] [Indexed: 02/28/2025] Open
Abstract
Knowledge graphs have been a useful tool for many biomedical applications because of their effective representation of biological concepts. Plentiful evidence exists linking the gut microbiome to disease in a correlative context, but uncovering the mechanistic explanation for those associations remains a challenge. Here we demonstrate the potential of knowledge graphs to hypothesize plausible mechanistic accounts of host-microbe interactions in disease. We have constructed a knowledge graph of linked microbes, genes and metabolites called MGMLink, and, using a shortest path or template-based search through the graph and a novel path-prioritization methodology based on the structure of the knowledge graph, we show that this knowledge supports inference of mechanistic hypotheses that explain observed relationships between microbes and disease phenotypes. We discuss specific applications of this methodology in inflammatory bowel disease and Parkinson's disease. This approach enables mechanistic hypotheses surrounding the complex interactions between gut microbes and disease to be generated in a scalable and comprehensive manner.
Collapse
Affiliation(s)
- Brook E Santangelo
- Department of Biomedical Informatics, University of Colorado Denver Anschutz Medical Campus, Aurora, CO, USA.
| | - Michael Bada
- Department of Pediatrics, University of Chicago, Chicago, IL, USA
| | | | - Catherine Lozupone
- Department of Biomedical Informatics, University of Colorado Denver Anschutz Medical Campus, Aurora, CO, USA
| |
Collapse
|
2
|
Hadinugroho W, Tjahjono Y, Foe K, Esar SY, Caroline C, Jessica MA, Wijaya H. Characterization of 2-((4-(chloromethyl)benzoyl)oxy)benzoate acid for analgesic tablet dosage form formulation. CURRENT RESEARCH IN PHARMACOLOGY AND DRUG DISCOVERY 2024; 7:100200. [PMID: 39314230 PMCID: PMC11417518 DOI: 10.1016/j.crphar.2024.100200] [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: 10/08/2023] [Revised: 08/01/2024] [Accepted: 09/02/2024] [Indexed: 09/25/2024] Open
Abstract
The 2-((4-(chloromethyl)benzoyl)oxy)benzoic acid (4CH2Cl) is a potential analgesic compound derived from salicylic acid and 4-chloromethyl benzoyl chloride. Characterization required 4CH2Cl for the formulation of tablet dosage forms. This study aims investigate the effect of SSG, PVP-K30, and the combination of SSG*PVP K-30 on the formulation of 4CH2Cl tablets. Additionally, this study aimed to obtain the optimum 4CH2Cl tablet composition. The experiment followed the two-factor simplex lattice design and direct compression method. The analgesic activity of 4CH2Cl in the optimal tablet was investigated using the hot-plate methods. The ANOVA of linear models is acceptable and the polynomial coefficients of quadratic models are similar to those of linear models. The coefficient of the linear model shows that SSG and PVP K-30 increase the Carr index (16.26; 20.61), Hausner ratio (1.19; 1.29), hardness (4.19; 9.39), friability (0.48; 0.67), disintegration time (0.34; 7.50), and drug release (85.29; 97.69). The coefficient of the quadratic model shows that SSG*PVP K-30 increased the Carr index (1.90), Hausner ratio (0.04), hardness (1.88), friability (0.06), and drug release (4.56), and decreased disintegration time (-0.30). SSG and PVP K-30 increased Carr index, Hausner ratio, hardness, friability, disintegration time, and drug release. The combination of SSG*PVP K-30 has the same effect, except that the disintegration time decreased. The optimum tablet formula is 4CH2Cl (300 mg), Ne (75 mg), SSG (33.60 mg), PVP K-30 (22.40 mg), MCC (40 mg), and SDL (up to 800 mg). 4CH2Cl tablets can be a candidate and choice for new analgesic drugs in the future.
Collapse
Affiliation(s)
- Wuryanto Hadinugroho
- Faculty of Pharmacy, Widya Mandala Surabaya Catholic University, Surabaya, 60112, Indonesia
| | - Yudy Tjahjono
- Faculty of Pharmacy, Widya Mandala Surabaya Catholic University, Surabaya, 60112, Indonesia
| | - Kuncoro Foe
- Faculty of Pharmacy, Widya Mandala Surabaya Catholic University, Surabaya, 60112, Indonesia
| | - Senny Yesery Esar
- Faculty of Pharmacy, Widya Mandala Surabaya Catholic University, Surabaya, 60112, Indonesia
| | - Caroline Caroline
- Faculty of Pharmacy, Widya Mandala Surabaya Catholic University, Surabaya, 60112, Indonesia
| | | | - Hendy Wijaya
- Faculty of Pharmacy, Widya Mandala Surabaya Catholic University, Surabaya, 60112, Indonesia
| |
Collapse
|
3
|
Santangelo B, Bada M, Hunter L, Lozupone C. Hypothesizing mechanistic links between microbes and disease using knowledge graphs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.01.569645. [PMID: 38106100 PMCID: PMC10723325 DOI: 10.1101/2023.12.01.569645] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Knowledge graphs have found broad biomedical applications, providing useful representations of complex knowledge. Although plentiful evidence exists linking the gut microbiome to disease, mechanistic understanding of those relationships remains generally elusive. Here we demonstrate the potential of knowledge graphs to hypothesize plausible mechanistic accounts of host-microbe interactions in disease. To do so, we constructed a knowledge graph of linked microbes, genes and metabolites called MGMLink. Using a semantically constrained shortest path search through the graph and a novel path prioritization methodology based on cosine similarity, we show that this knowledge supports inference of mechanistic hypotheses that explain observed relationships between microbes and disease phenotypes. We discuss specific applications of this methodology in inflammatory bowel disease and Parkinson's disease. This approach enables mechanistic hypotheses surrounding the complex interactions between gut microbes and disease to be generated in a scalable and comprehensive manner.
Collapse
|
4
|
Qasem A, Assaggaf H, Mrabti HN, Minshawi F, Rajab BS, Attar AA, Alyamani RA, Hamed M, Mrabti NN, Baaboua AE, Omari NE, Alshahrani MM, Awadh AAA, Sheikh RA, Ming LC, Goh KW, Bouyahya A. Determination of Chemical Composition and Investigation of Biological Activities of Ocimum basilicum L. Molecules 2023; 28:614. [PMID: 36677672 PMCID: PMC9866482 DOI: 10.3390/molecules28020614] [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: 09/02/2022] [Revised: 10/08/2022] [Accepted: 10/12/2022] [Indexed: 01/11/2023] Open
Abstract
This study aimed to determine the chemical composition of the essential oils (EOs) of Ocimum basilicum L., as well as to evaluate the antibacterial, antidiabetic, dermatoprotective, and anti-inflammatory properties, and the EOs and aqueous extracts of O. basilicum. The antibacterial activity was evaluated against bacterial strains, Gram-positive and Gram-negative, using the well diffusion and microdilution methods, whereas the antidiabetic activity was assessed in vitro using two enzymes involved in carbohydrate digestion, α-amylase and α-glucosidase. On the other hand, the dermatoprotective and anti-inflammatory activities were studied by testing tyrosinase and lipoxygenase inhibition activity, respectively. The results showed that the chemical composition of O. basilicum EO (OBEO) is dominated by methyl chavicol (86%) and trans-anethol (8%). OBEO exhibited significant antibacterial effects against Gram-negative and Gram-positive strains, demonstrated by considerable diameters of the inhibition zones and lower MIC and MBC values. In addition, OBEO exhibited significant inhibition of α-amylase (IC50 = 50.51 ± 0.32 μg/mL) and α-glucosidase (IC50 = 39.84 ± 1.2 μg/mL). Concerning the anti-inflammatory activity, OBEO significantly inhibited lipoxygenase activity (IC50 = 18.28 ± 0.03 μg/mL) compared to the aqueous extract (IC50 = 24.8 ± 0.01 μg/mL). Moreover, tyrosinase was considerably inhibited by OBEO (IC50 = 68.58 ± 0.03 μg/mL) compared to the aqueous extract (IC50 = 118.37 ± 0.05 μg/mL). The toxicological investigations revealed the safety of O. basilicum in acute and chronic toxicity. The finding of in silico analysis showed that methyl chavicol and trans-anethole (main compounds of OBEO) validate the pharmacokinetics of these compounds and decipher some antibacterial targets.
Collapse
Affiliation(s)
- Ahmed Qasem
- Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Hamza Assaggaf
- Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Hanae Naceiri Mrabti
- Laboratoires TBC, Faculty of Pharmaceutical and Biological Sciences, B.P. 8359006 Lille, France
| | - Faisal Minshawi
- Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Bodour S. Rajab
- Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Ammar A. Attar
- Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Reema A. Alyamani
- Faculty of Applied Medical Sciences, Clinical Nutrition Department, Umm Al-Qura University, Makkah 24381, Saudi Arabia
| | - Munerah Hamed
- Department of Pathology, Faculty of Medicine, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Nidal Naceiri Mrabti
- Engineering Materials, Modeling and Environmental Laboratory, Faculty of Sciences Dhar El Mehraz, Sidi Mohammed Ben Abdellah University, Fez 30000, Morocco
| | - Aicha El Baaboua
- Biology and Health Laboratory, Department of Biology, Faculty of Science, Abdelmalek-Essaadi University, Tetouan 93000, Morocco
| | - Nasreddine El Omari
- Laboratory of Histology, Embryology and Cytogenetic, Faculty of Medicine and Pharmacy, Mohammed V University in Rabat, Rabat 10100, Morocco
| | - Mohammed Merae Alshahrani
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Najran University, P.O. Box 1988, Najran 61441, Saudi Arabia
| | - Ahmed Abdullah Al Awadh
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Najran University, P.O. Box 1988, Najran 61441, Saudi Arabia
| | - Ryan Adnan Sheikh
- Biochemistry Department, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Long Chiau Ming
- School of Medical and Life Sciences, Sunway University, Bandar Sunway 47500, Malaysia
| | - Khang Wen Goh
- Faculty of Data Science and Information Technology, INTI International University, Nilai 71800, Malaysia
| | - Abdelhakim Bouyahya
- Laboratory of Human Pathologies Biology, Department of Biology, Faculty of Sciences, Mohammed V University in Rabat, Rabat 10100, Morocco
| |
Collapse
|
5
|
Hadinugroho W, Foe K, Tjahjono Y, Caroline C, Esar SY, Wijaya H, Jessica MA. Tablet Formulation of 2-((3-(Chloromethyl)benzoyl)oxy)benzoic Acid by Linear and Quadratic Models. ACS OMEGA 2022; 7:34045-34053. [PMID: 36188286 PMCID: PMC9520729 DOI: 10.1021/acsomega.2c03147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 08/17/2022] [Indexed: 06/16/2023]
Abstract
PURPOSE This research determines the effect of sodium lauryl sulfate (SLS) as a surfactant, croscarmellose sodium (CS) as a disintegrating agent, and SLS-CS combinations on 2-((3-(chloromethyl)benzoyl)oxy)benzoic acid (3CH2Cl) (log P = 3.73) tablet formulations. In addition, this study aims to determine the optimum of the 3CH2Cl tablet formula. METHODS The tablets are manufactured through direct compression according to the simplex lattice design. The optimal SLS and CS concentration was determined in vitro using linear and quadratic models to achieve better tablet disintegration and dissolution. RESULTS The same linear and quadratic coefficient profiles of SLS and CS indicate that the combined coefficient of SLS-CS with a quadratic model can be used to predict the effect of the SLS-CS combination. Based on the linear model coefficients, SLS and CS increase the value of flow time (9.35; 7.65), Carr index (26.17; 21.17), hardness (9.84; 7.44), friability (0.38; 0.31), disintegrating time (5.74; 2.62), and drug release (84.28; 58.65). The quadratic model coefficient shows that SLS-CS combinations increase flow time (0.60), Carr index (2.00), hardness (1.00), and disintegrating time (1.04). Meanwhile, they decrease friability (-0.02) and drug release (-9.10). CONCLUSIONS SLS, CS, and SLS-CS combinations affect the quality of tablet mass and tablets. The optimum tablet formula was 3CH2Cl (300 mg), Ne (9.38%), SLS (0.92%), CS (2.33%), MCC (5%), and SDL (ad 800 mg). 3CH2Cl has analgesic activity despite the presence of tablet excipients. The 3CH2Cl tablet is an innovative formulation and a new alternative for future analgesic drugs.
Collapse
Affiliation(s)
- Wuryanto Hadinugroho
- Faculty of Pharmacy, Widya Mandala Surabaya Catholic University, Kalisari Selatan no. 1 Pakuwon City, Surabaya 60112, Indonesia
| | - Kuncoro Foe
- Faculty of Pharmacy, Widya Mandala Surabaya Catholic University, Kalisari Selatan no. 1 Pakuwon City, Surabaya 60112, Indonesia
| | - Yudy Tjahjono
- Faculty of Pharmacy, Widya Mandala Surabaya Catholic University, Kalisari Selatan no. 1 Pakuwon City, Surabaya 60112, Indonesia
| | - Caroline Caroline
- Faculty of Pharmacy, Widya Mandala Surabaya Catholic University, Kalisari Selatan no. 1 Pakuwon City, Surabaya 60112, Indonesia
| | - Senny Yesery Esar
- Faculty of Pharmacy, Widya Mandala Surabaya Catholic University, Kalisari Selatan no. 1 Pakuwon City, Surabaya 60112, Indonesia
| | - Hendy Wijaya
- Faculty of Pharmacy, Widya Mandala Surabaya Catholic University, Kalisari Selatan no. 1 Pakuwon City, Surabaya 60112, Indonesia
| | - Maria Annabella Jessica
- Faculty of Pharmacy, Widya Mandala Surabaya Catholic University, Kalisari Selatan no. 1 Pakuwon City, Surabaya 60112, Indonesia
| |
Collapse
|
6
|
Son HK, Kim BH, Lee J, Park S, Oh CB, Jung S, Lee JK, Ha JH. Partial Replacement of Dietary Fat with Krill Oil or Coconut Oil Alleviates Dyslipidemia by Partly Modulating Lipid Metabolism in Lipopolysaccharide-Injected Rats on a High-Fat Diet. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:843. [PMID: 35055664 PMCID: PMC8775371 DOI: 10.3390/ijerph19020843] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/06/2022] [Accepted: 01/08/2022] [Indexed: 02/04/2023]
Abstract
This study investigated the effects of partial replacement of dietary fat with krill oil (KO) or coconut oil (CO) on dyslipidemia and lipid metabolism in rats fed with a high-fat diet (HFD). Sprague Dawley rats were divided into three groups as follows: HFD, HFD + KO, and HFD + CO. The rats were fed each diet for 10 weeks and then intraperitoneally injected with phosphate-buffered saline (PBS) or lipopolysaccharide (LPS) (1 mg/kg). The KO- and CO-fed rats exhibited lower levels of serum lipids and aspartate aminotransferases than those of the HFD-fed rats. Rats fed with HFD + KO displayed significantly lower hepatic histological scores and hepatic triglyceride (TG) content than rats fed with HFD. The KO supplementation also downregulated the adipogenic gene expression in the liver. When treated with LPS, the HFD + KO and HFD + CO groups reduced the adipocyte size in the epididymal white adipose tissues (EAT) relative to the HFD group. These results suggest that KO and CO could improve lipid metabolism dysfunction.
Collapse
Affiliation(s)
- Hee-Kyoung Son
- Research Center for Industrialization of Natural Neutralization, Dankook University, Cheonan 31116, Korea; (H.-K.S.); (J.L.); (S.P.); (S.J.)
| | - Bok-Hee Kim
- Department of Food and Nutrition, Chosun University, Gwangju 61452, Korea;
| | - Jisu Lee
- Research Center for Industrialization of Natural Neutralization, Dankook University, Cheonan 31116, Korea; (H.-K.S.); (J.L.); (S.P.); (S.J.)
- Department of Food Science and Nutrition, Dankook University, Cheonan 31116, Korea
| | - Seohyun Park
- Research Center for Industrialization of Natural Neutralization, Dankook University, Cheonan 31116, Korea; (H.-K.S.); (J.L.); (S.P.); (S.J.)
- Department of Food Science and Nutrition, Dankook University, Cheonan 31116, Korea
| | - Chung-Bae Oh
- Office of Technical Liaison, Industry Support Team, Gyeongnam Branch Institute, Korea Institute of Toxicology, Jinju 52834, Korea;
| | - Sunyoon Jung
- Research Center for Industrialization of Natural Neutralization, Dankook University, Cheonan 31116, Korea; (H.-K.S.); (J.L.); (S.P.); (S.J.)
- Department of Food Science and Nutrition, Dankook University, Cheonan 31116, Korea
| | - Jennifer K. Lee
- Food Science and Human Nutrition Department, University of Florida, Gainesville, FL 32611, USA
| | - Jung-Heun Ha
- Research Center for Industrialization of Natural Neutralization, Dankook University, Cheonan 31116, Korea; (H.-K.S.); (J.L.); (S.P.); (S.J.)
- Department of Food Science and Nutrition, Dankook University, Cheonan 31116, Korea
| |
Collapse
|