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Moetlediwa MT, Jack BU, Mazibuko-Mbeje SE, Pheiffer C, Titinchi SJJ, Salifu EY, Ramharack P. Evaluating the Therapeutic Potential of Curcumin and Synthetic Derivatives: A Computational Approach to Anti-Obesity Treatments. Int J Mol Sci 2024; 25:2603. [PMID: 38473849 DOI: 10.3390/ijms25052603] [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: 12/15/2023] [Revised: 01/30/2024] [Accepted: 02/09/2024] [Indexed: 03/14/2024] Open
Abstract
Natural compounds such as curcumin, a polyphenolic compound derived from the rhizome of turmeric, have gathered remarkable scientific interest due to their diverse metabolic benefits including anti-obesity potential. However, curcumin faces challenges stemming from its unfavorable pharmacokinetic profile. To address this issue, synthetic curcumin derivatives aimed at enhancing the biological efficacy of curcumin have previously been developed. In silico modelling techniques have gained significant recognition in screening synthetic compounds as drug candidates. Therefore, the primary objective of this study was to assess the pharmacokinetic and pharmacodynamic characteristics of three synthetic derivatives of curcumin. This evaluation was conducted in comparison to curcumin, with a specific emphasis on examining their impact on adipogenesis, inflammation, and lipid metabolism as potential therapeutic targets of obesity mechanisms. In this study, predictive toxicity screening confirmed the safety of curcumin, with the curcumin derivatives demonstrating a safe profile based on their LD50 values. The synthetic curcumin derivative 1A8 exhibited inactivity across all selected toxicity endpoints. Furthermore, these compounds were deemed viable candidate drugs as they adhered to Lipinski's rules and exhibited favorable metabolic profiles. Molecular docking studies revealed that both curcumin and its synthetic derivatives exhibited favorable binding scores, whilst molecular dynamic simulations showed stable binding with peroxisome proliferator-activated receptor gamma (PPARγ), csyclooxygenase-2 (COX2), and fatty acid synthase (FAS) proteins. The binding free energy calculations indicated that curcumin displayed potential as a strong regulator of PPARγ (-60.2 ± 0.4 kcal/mol) and FAS (-37.9 ± 0.3 kcal/mol), whereas 1A8 demonstrated robust binding affinity with COX2 (-64.9 ± 0.2 kcal/mol). In conclusion, the results from this study suggest that the three synthetic curcumin derivatives have similar molecular interactions to curcumin with selected biological targets. However, in vitro and in vivo experimental studies are recommended to validate these findings.
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Affiliation(s)
- Marakiya T Moetlediwa
- Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg 7505, South Africa
- Department of Biochemistry, North-West University, Mmabatho 2745, South Africa
| | - Babalwa U Jack
- Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg 7505, South Africa
| | | | - Carmen Pheiffer
- Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg 7505, South Africa
- Department of Obstetrics and Gynaecology, Faculty of Health Sciences, University of Pretoria, Pretoria 0001, South Africa
| | - Salam J J Titinchi
- Department of Chemistry, Faculty of Natural Science, University of the Western Cape, Bellville 7535, South Africa
| | - Elliasu Y Salifu
- Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg 7505, South Africa
| | - Pritika Ramharack
- Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg 7505, South Africa
- Pharmaceutical Sciences, School of Health Sciences, University of KwaZulu-Natal, Westville, Durban 4001, South Africa
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Naji SA, Sağlik BN, Agamennone M, Evren AE, Gundogdu-Karaburun N, Karaburun AÇ. Design and Evaluation of Synthesized Pyrrole Derivatives as Dual COX-1 and COX-2 Inhibitors Using FB-QSAR Approach. ACS OMEGA 2023; 8:48884-48903. [PMID: 38162789 PMCID: PMC10753557 DOI: 10.1021/acsomega.3c06344] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 11/16/2023] [Accepted: 11/17/2023] [Indexed: 01/03/2024]
Abstract
This study delves into the intricate dynamics of the inflammatory response, unraveling the pivotal role played by cyclooxygenase (COX) enzymes, particularly COX-1 and COX-2 subtypes. Motivated by the pursuit of advancing scientific knowledge, our contribution to this field is marked by the design and synthesis of novel pyrrole derivatives. Crafted as potential inhibitors of COX-1 and COX-2 enzymes, our goal was to unearth molecules with heightened efficacy in modulating enzyme activity. A meticulous exploration of a synthesis library, housing around 3000 compounds, expedited the identification of potent candidates. Employing advanced docking studies and field-based Quantitative Structure-Activity Relationship (FB-QSAR) analyses enriched our understanding of the complex interactions between synthesized compounds and COX enzymes. Guided by FB-QSAR insights, our synthesis path led to the identification of compounds 4g, 4h, 4l, and 4k as potent COX-2 inhibitors, surpassing COX-1 efficacy. Conversely, compounds 5b and 5e exhibited heightened inhibitory activity against COX-1 relative to COX-2. The utilization of pyrrole derivatives as COX enzyme inhibitors holds promise for groundbreaking advancements in the domain of anti-inflammatory therapeutics, presenting avenues for innovative pharmaceutical exploration.
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Affiliation(s)
- Shoruq Ahmed Naji
- Faculty
of Pharmacy, Department of Pharmaceutical Chemistry, Anadolu University, 26470 Eskişehir, Turkey
| | - Begüm Nurpelin Sağlik
- Faculty
of Pharmacy, Department of Pharmaceutical Chemistry, Anadolu University, 26470 Eskişehir, Turkey
| | - Mariangela Agamennone
- Department
of Pharmacy, University “G. d’Annunzio”
of Chieti-Pescara, Via
dei Vestini 31, 66100 Chieti, Italy
| | - Asaf Evrim Evren
- Faculty
of Pharmacy, Department of Pharmaceutical Chemistry, Anadolu University, 26470 Eskişehir, Turkey
- Vocational
School of Health Services, Pharmacy Services, Bilecik Seyh Edebali University, 11230 Bilecik, Turkey
| | - Nalan Gundogdu-Karaburun
- Faculty
of Pharmacy, Department of Pharmaceutical Chemistry, Anadolu University, 26470 Eskişehir, Turkey
| | - Ahmet Çagrı Karaburun
- Faculty
of Pharmacy, Department of Pharmaceutical Chemistry, Anadolu University, 26470 Eskişehir, Turkey
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Chakravarti SK, Alla SRM. Descriptor Free QSAR Modeling Using Deep Learning With Long Short-Term Memory Neural Networks. Front Artif Intell 2019; 2:17. [PMID: 33733106 PMCID: PMC7861338 DOI: 10.3389/frai.2019.00017] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Accepted: 08/22/2019] [Indexed: 12/15/2022] Open
Abstract
Current practice of building QSAR models usually involves computing a set of descriptors for the training set compounds, applying a descriptor selection algorithm and finally using a statistical fitting method to build the model. In this study, we explored the prospects of building good quality interpretable QSARs for big and diverse datasets, without using any pre-calculated descriptors. We have used different forms of Long Short-Term Memory (LSTM) neural networks to achieve this, trained directly using either traditional SMILES codes or a new linear molecular notation developed as part of this work. Three endpoints were modeled: Ames mutagenicity, inhibition of P. falciparum Dd2 and inhibition of Hepatitis C Virus, with training sets ranging from 7,866 to 31,919 compounds. To boost the interpretability of the prediction results, attention-based machine learning mechanism, jointly with a bidirectional LSTM was used to detect structural alerts for the mutagenicity data set. Traditional fragment descriptor-based models were used for comparison. As per the results of the external and cross-validation experiments, overall prediction accuracies of the LSTM models were close to the fragment-based models. However, LSTM models were superior in predicting test chemicals that are dissimilar to the training set compounds, a coveted quality of QSAR models in real world applications. In summary, it is possible to build QSAR models using LSTMs without using pre-computed traditional descriptors, and models are far from being "black box." We wish that this study will be helpful in bringing large, descriptor-less QSARs to mainstream use.
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Chakravarti SK. Distributed Representation of Chemical Fragments. ACS OMEGA 2018; 3:2825-2836. [PMID: 30023852 PMCID: PMC6044751 DOI: 10.1021/acsomega.7b02045] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 02/23/2018] [Indexed: 06/08/2023]
Abstract
This article describes an unsupervised machine learning method for computing distributed vector representation of molecular fragments. These vectors encode fragment features in a continuous high-dimensional space and enable similarity computation between individual fragments, even for small fragments with only two heavy atoms. The method is based on a word embedding algorithm borrowed from natural language processing field, and approximately 6 million unlabeled PubChem chemicals were used for training. The resulting dense fragment vectors are in contrast to the traditional sparse "one-hot" fragment representation and capture rich relational structure in the fragment space. The vectors of small linear fragments were averaged to yield distributed vectors of bigger fragments and molecules, which were used for different tasks, e.g., clustering, ligand recall, and quantitative structure-activity relationship modeling. The distributed vectors were found to be better at clustering ring systems and recall of kinase ligands as compared to standard binary fingerprints. This work demonstrates unsupervised learning of fragment chemistry from large sets of unlabeled chemical structures and subsequent application to supervised training on relatively small data sets of labeled chemicals.
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Kronenberger T, Windshügel B, Wrenger C, Honorio KM, Maltarollo VG. On the relationship of anthranilic derivatives structure and the FXR (Farnesoid X receptor) agonist activity. J Biomol Struct Dyn 2018; 36:4378-4391. [DOI: 10.1080/07391102.2017.1417161] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Thales Kronenberger
- Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
- Fraunhofer Institute for Molecular Biology und Applied Ecology IME, Hamburg, Germany
| | - Björn Windshügel
- Fraunhofer Institute for Molecular Biology und Applied Ecology IME, Hamburg, Germany
| | - Carsten Wrenger
- Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Kathia M. Honorio
- Center for Natural Sciences and Humanities, ABC Federal University, Santo André, São Paulo, Brazil
- School of Arts, Sciences and Humanities, University of São Paulo, São Paulo, Brazil
| | - Vinicius G. Maltarollo
- Department of Pharmaceutical Products, Faculty of Pharmacy, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
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Meghani NM, Amin HH, Lee BJ. Mechanistic applications of click chemistry for pharmaceutical drug discovery and drug delivery. Drug Discov Today 2017; 22:1604-1619. [PMID: 28754291 DOI: 10.1016/j.drudis.2017.07.007] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 06/18/2017] [Accepted: 07/17/2017] [Indexed: 01/30/2023]
Abstract
The concept of click chemistry (CC), first introduced by K.B. Sharpless, has been widely adopted for use in drug discovery, novel drug delivery systems (DDS), polymer chemistry, and material sciences. In this review, we outline novel aspects of CC related to drug discovery and drug delivery, with a brief overview of molecular mechanisms underlying each click reaction commonly used by researchers, and the main patents that paved the way for further diverse medicinal applications. We also describe recent progress in drug discovery and polymeric and carbon material-based drug delivery for potential pharmaceutical applications and advancements based on the CC approach, and discuss some intrinsic limitations of this popular conjugation reaction. The use of CC is likely to significantly advance drug discovery and bioconjugation development.
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Affiliation(s)
- Nilesh M Meghani
- College of Pharmacy, Ajou University, Suwon 16499, Republic of Korea
| | - Hardik H Amin
- College of Pharmacy, Ajou University, Suwon 16499, Republic of Korea
| | - Beom-Jin Lee
- College of Pharmacy, Ajou University, Suwon 16499, Republic of Korea; Institute of Pharmaceutical Science and Technology, Ajou University, Suwon 16499, Republic of Korea.
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7
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Understanding PPAR-δ affinity and selectivity using hologram quantitative structure-activity modeling, molecular docking and GRID calculations. Future Med Chem 2016; 8:1913-1926. [PMID: 27689854 DOI: 10.4155/fmc-2016-0061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
AIM Type 2 diabetes mellitus and metabolic syndrome are two diseases related to disorders of lipid and carbohydrate metabolism and insulin resistance. Peroxisome proliferator-activated receptors (PPARs) are a class of nuclear receptors that control the metabolism of lipids/carbohydrates and are considered targets for both diseases. PPAR affinity and selectivity are critical points to design drug candidates with appropriated pharmacodynamic/kinetic profiles. MATERIALS & METHODS Hologram quantitative structure-activity relationships studies were conducted, as well molecular docking and molecular interaction field calculations, in order to explain affinity and selectivity of selected compounds. RESULTS The constructed hologram quantitative structure-activity relationship models are robust and predictive (values of q2 and r2test above 0.70). CONCLUSION The quantitative structure-activity relationship models and docking/GRID analyses indicated that carboxyl group of indole-sulfonamide derivatives could interact at helix-3 region, being considered important point of PPAR-δ selectivity.
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Zou JW, Huang M, Huang JX, Hu GX, Jiang YJ. Quantitative structure–hydrophobicity relationships of molecular fragments and beyond. J Mol Graph Model 2016; 64:110-120. [DOI: 10.1016/j.jmgm.2016.01.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 01/13/2016] [Accepted: 01/19/2016] [Indexed: 10/22/2022]
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Hologram QSAR studies of antiprotozoal activities of sesquiterpene lactones. Molecules 2014; 19:10546-62. [PMID: 25045893 PMCID: PMC6271290 DOI: 10.3390/molecules190710546] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Revised: 07/08/2014] [Accepted: 07/09/2014] [Indexed: 11/26/2022] Open
Abstract
Infectious diseases such as trypanosomiasis and leishmaniasis are considered neglected tropical diseases due the lack for many years of research and development into new drug treatments besides the high incidence of mortality and the lack of current safe and effective drug therapies. Natural products such as sesquiterpene lactones have shown activity against T. brucei and L. donovani, the parasites responsible for these neglected diseases. To evaluate structure activity relationships, HQSAR models were constructed to relate a series of 40 sesquiterpene lactones (STLs) with activity against T. brucei, T. cruzi, L. donovani and P. falciparum and also with their cytotoxicity. All constructed models showed good internal (leave-one-out q2 values ranging from 0.637 to 0.775) and external validation coefficients (r2test values ranging from 0.653 to 0.944). From HQSAR contribution maps, several differences between the most and least potent compounds were found. The fragment contribution of PLS-generated models confirmed the results of previous QSAR studies that the presence of α,β-unsatured carbonyl groups is fundamental to biological activity. QSAR models for the activity of these compounds against T. cruzi, L. donovani and P. falciparum are reported here for the first time. The constructed HQSAR models are suitable to predict the activity of untested STLs.
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10
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Thirumurugan P, Matosiuk D, Jozwiak K. Click Chemistry for Drug Development and Diverse Chemical–Biology Applications. Chem Rev 2013; 113:4905-79. [DOI: 10.1021/cr200409f] [Citation(s) in RCA: 1309] [Impact Index Per Article: 119.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Prakasam Thirumurugan
- Laboratory
of Medical Chemistry and Neuroengineering, Department of Chemistry, and ‡Department of
Synthesis and Chemical Technology of Pharmaceutical Substances, Medical University of Lublin, Lublin
20093, Poland
| | - Dariusz Matosiuk
- Laboratory
of Medical Chemistry and Neuroengineering, Department of Chemistry, and ‡Department of
Synthesis and Chemical Technology of Pharmaceutical Substances, Medical University of Lublin, Lublin
20093, Poland
| | - Krzysztof Jozwiak
- Laboratory
of Medical Chemistry and Neuroengineering, Department of Chemistry, and ‡Department of
Synthesis and Chemical Technology of Pharmaceutical Substances, Medical University of Lublin, Lublin
20093, Poland
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11
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A fragment-based approach for ligand binding affinity and selectivity for the liver X receptor beta. J Mol Graph Model 2012; 32:19-31. [DOI: 10.1016/j.jmgm.2011.09.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2011] [Revised: 09/21/2011] [Accepted: 09/25/2011] [Indexed: 11/22/2022]
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12
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Shao L, Wu L, Fan X, Cheng Y. Consensus ranking approach to understanding the underlying mechanism with QSAR. J Chem Inf Model 2010; 50:1941-8. [PMID: 21049968 DOI: 10.1021/ci100305g] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Constructing a highly predictive model and exploiting the underlying mechanism associated with a specific property of chemicals are the two main goals of quantitative structure-activity relationship analysis (QSAR). However, the latter has long been carried out as a byproduct of model construction. Here we confirmed for the first time in this study that conventional descriptor selection methods designed to develop a best predictive model are likely not suitable for mechanistic analysis, i.e., the selected descriptors strongly depended on the selection of chemicals in the training sets. As an alternative, a consensus ranking protocol was proposed to select a robust descriptor set for mechanistic analysis, which can successfully overcome the above shortcoming. Moreover, the consistently inferior model performance using descriptors selected for mechanistic analysis suggested the irreplaceable role of model development in achieving models with the best predictive capability.
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Affiliation(s)
- Li Shao
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
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Salum LB, Valadares NF. Fragment-guided approach to incorporating structural information into a CoMFA study: BACE-1 as an example. J Comput Aided Mol Des 2010; 24:803-17. [DOI: 10.1007/s10822-010-9375-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2010] [Accepted: 07/15/2010] [Indexed: 12/27/2022]
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