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Pan G, Chai L, Chen R, Yuan Q, Song Z, Feng W, Wei J, Yang Z, Zhang Y, Xie G, Yan A, Lv Q, Wang C, Zhao Y, Wang Y. Potential mechanism of Qinggong Shoutao pill alleviating age-associated memory decline based on integration strategy. PHARMACEUTICAL BIOLOGY 2024; 62:105-119. [PMID: 38145345 PMCID: PMC10763866 DOI: 10.1080/13880209.2023.2291689] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 11/30/2023] [Indexed: 12/26/2023]
Abstract
CONTEXT Qinggong Shoutao Wan (QGSTW) is a pill used as a traditional medicine to treat age-associated memory decline (AAMI). However, its potential mechanisms are unclear. OBJECTIVE This study elucidates the possible mechanisms of QGSTW in treating AAMI. MATERIALS AND METHODS Network pharmacology and molecular docking approaches were utilized to identify the potential pathway by which QGSTW alleviates AAMI. C57BL/6J mice were divided randomly into control, model, and QGSTW groups. A mouse model of AAMI was established by d-galactose, and the pathways that QGSTW acts on to ameliorate AAMI were determined by ELISA, immunofluorescence staining and Western blotting after treatment with d-gal (100 mg/kg) and QGSTW (20 mL/kg) for 12 weeks. RESULTS Network pharmacology demonstrated that the targets of the active components were significantly enriched in the cAMP signaling pathway. AKT1, FOS, GRIN2B, and GRIN1 were the core target proteins. QGSTW treatment increased the discrimination index from -16.92 ± 7.06 to 23.88 ± 15.94% in the novel location test and from -19.54 ± 5.71 to 17.55 ± 6.73% in the novel object recognition test. ELISA showed that QGSTW could increase the levels of cAMP. Western blot analysis revealed that QGSTW could upregulate the expression of PKA, CREB, c-Fos, GluN1, GluA1, CaMKII-α, and SYN. Immunostaining revealed that the expression of SYN was decreased in the CA1 and DG. DISCUSSION AND CONCLUSIONS This study not only provides new insights into the mechanism of QGSTW in the treatment of AAMI but also provides important information and new research ideas for the discovery of traditional Chinese medicine compounds that can treat AAMI.
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Affiliation(s)
- Guiyun Pan
- Tianjin University of Traditional Chinese Medicine, Tianjin, China
- Second Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Lijuan Chai
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Rui Chen
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Qing Yuan
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Zhihui Song
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Wanying Feng
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Jinna Wei
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Zhihua Yang
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Yuhang Zhang
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Guinan Xie
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - An Yan
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Qingbo Lv
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Caijun Wang
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Yingqiang Zhao
- Second Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Yi Wang
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
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2
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Roggia M, Natale B, Amendola G, Grasso N, Di Maro S, Taliani S, Castellano S, Reina SCR, Salvati E, Amato J, Cosconati S. Discovering Dually Active Anti-cancer Compounds with a Hybrid AI-structure-based Approach. J Chem Inf Model 2024. [PMID: 39276072 DOI: 10.1021/acs.jcim.4c01132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/16/2024]
Abstract
Cancer's persistent growth often relies on its ability to maintain telomere length and tolerate the accumulation of DNA damage. This study explores a computational approach to identify compounds that can simultaneously target both G-quadruplex (G4) structures and poly(ADP-ribose) polymerase (PARP)1 enzyme, offering a potential multipronged attack on cancer cells. We employed a hybrid virtual screening (VS) protocol, combining the power of machine learning with traditional structure-based methods. PyRMD, our AI-powered tool, was first used to analyze vast chemical libraries and to identify potential PARP1 inhibitors based on known bioactivity data. Subsequently, a structure-based VS approach selected compounds from these identified inhibitors for their G4 stabilization potential. This two-step process yielded 50 promising candidates, which were then experimentally validated for their ability to inhibit PARP1 and stabilize G4 structures. Ultimately, four lead compounds emerged as promising candidates with the desired dual activity and demonstrated antiproliferative effects against specific cancer cell lines. This study highlights the potential of combining Artificial Intelligence and structure-based methods for the discovery of multitarget anticancer compounds, offering a valuable approach for future drug development efforts.
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Affiliation(s)
- Michele Roggia
- DiSTABiF, Università della Campania Luigi Vanvitelli, Via Vivaldi 43, Caserta 81100, Italy
| | - Benito Natale
- DiSTABiF, Università della Campania Luigi Vanvitelli, Via Vivaldi 43, Caserta 81100, Italy
| | - Giorgio Amendola
- DiSTABiF, Università della Campania Luigi Vanvitelli, Via Vivaldi 43, Caserta 81100, Italy
| | - Nicola Grasso
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, Naples 80131, Italy
| | - Salvatore Di Maro
- DiSTABiF, Università della Campania Luigi Vanvitelli, Via Vivaldi 43, Caserta 81100, Italy
| | - Sabrina Taliani
- Department of Pharmacy, University of Pisa, Via Bonanno 6, Pisa 56126, Italy
| | - Sabrina Castellano
- Dipartimento di Farmacia, Università di Salerno, Via Giovanni Paolo II 132, 84084 Fisciano Salerno, Italy
| | | | - Erica Salvati
- Institute of Molecular Biology and Pathology, National Research Council, Rome, Italy
| | - Jussara Amato
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, Naples 80131, Italy
| | - Sandro Cosconati
- DiSTABiF, Università della Campania Luigi Vanvitelli, Via Vivaldi 43, Caserta 81100, Italy
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3
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Khazravi L, Hamedi J, Attar H, Ardjmand M. Nymphaea alba leaf powder effectiveness in removing nisin from fermentation broth using docking and experimental analysis. Sci Rep 2024; 14:20645. [PMID: 39232102 PMCID: PMC11375215 DOI: 10.1038/s41598-024-71513-0] [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: 09/13/2023] [Accepted: 08/28/2024] [Indexed: 09/06/2024] Open
Abstract
The accumulation of nisin in the fermentation medium can reduce the process's productivity. This research studied the potential of Nymphaea alba leaf powder (NALP) as a hydrophobic biosorbent for efficient in-situ nisin adsorption from the fermentation medium by docking and experimental analysis. Molecular docking analysis showed that di-galloyl ellagic acid, a phytochemical compound found in N. alba, had the highest affinity towards nisin. Enhancements in nisin adsorption were seen following pre-treatment of NAPL with HCl and MgCl2. A logistic growth model was employed to evaluate the growth dynamics of the biosorption capacity, offering valuable insights for process scalability. Furthermore, optimization through Response Surface Methodology elucidated optimal nisin desorption conditions by Liebig's law of the minimum, which posits that the scarcest resource governs production efficiency. Fourier Transform Infrared (FTIR) spectroscopy pinpointed vital functional groups involved in biosorption. Scanning electron microscopy revealed the changing physical characteristics of the biosorbent after exposure to nisin. The findings designate NALP as a feasible adsorbent for nisin removal from the fermentation broth, thus facilitating its application in the purification of other biotechnological products based on growth and production optimization principles.
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Affiliation(s)
- Leila Khazravi
- Department of Petroleum Engineering, Faculty of Petroleum and Chemical Engineering, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Javad Hamedi
- Department of Microbial Biotechnology, School of Biology, College of Science, University of Tehran, Tehran, Iran.
| | - Hossein Attar
- Department of Petroleum Engineering, Faculty of Petroleum and Chemical Engineering, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Mehdi Ardjmand
- Chemical Engineering Department, Islamic Azad University, South Tehran Branch, Tehran, Iran
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4
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Weller J, Rohs R. Structure-Based Drug Design with a Deep Hierarchical Generative Model. J Chem Inf Model 2024; 64:6450-6463. [PMID: 39058534 PMCID: PMC11350878 DOI: 10.1021/acs.jcim.4c01193] [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: 07/08/2024] [Revised: 07/16/2024] [Accepted: 07/17/2024] [Indexed: 07/28/2024]
Abstract
Recently, the remarkable growth of available crystal structure data and libraries of commercially available or readily synthesizable molecules have unlocked previously inaccessible regions of chemical space for drug development. Paired with improvements in virtual ligand screening methods, these expanded libraries are having a notable impact on early drug design efforts. Yet screening-based methods still face scalability limits, due to computational constraints and the sheer scale of drug-like space. Machine learning approaches are overcoming these limitations by learning the fundamental intra- and intermolecular relationships in drug-target systems from existing data. Here, we introduce DrugHIVE, a deep hierarchical variational autoencoder that outperforms state-of-the-art autoregressive and diffusion-based methods in both speed and performance on common generative benchmarks. DrugHIVE's hierarchical design enables improved control over molecular generation. Its capabilities include dramatically increasing virtual screening efficiency and accelerating a wide range of common drug design tasks, including de novo generation, molecular optimization, scaffold hopping, linker design, and high-throughput pattern replacement. Our highly scalable method can even be applied to receptors with high-confidence AlphaFold-predicted structures, extending the ability to generate high-quality drug-like molecules to a majority of the unsolved human proteome.
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Affiliation(s)
- Jesse
A. Weller
- Department
of Quantitative and Computational Biology, University of Southern California, Los Angeles, California 90089, United States
- Department
of Physics and Astronomy, University of
Southern California, Los Angeles, California 90089, United States
| | - Remo Rohs
- Department
of Quantitative and Computational Biology, University of Southern California, Los Angeles, California 90089, United States
- Department
of Physics and Astronomy, University of
Southern California, Los Angeles, California 90089, United States
- Department
of Chemistry, University of Southern California, Los Angeles, California 90089, United States
- Thomas
Lord Department of Computer Science, University
of Southern California, Los Angeles, California 90089, United States
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5
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Lokhandwala J, Matlack JK, Smalley TB, Miner RE, Tran TH, Binning JM. Structural basis for FN3K-mediated protein deglycation. Structure 2024:S0969-2126(24)00281-8. [PMID: 39173621 DOI: 10.1016/j.str.2024.07.018] [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: 02/16/2024] [Revised: 06/05/2024] [Accepted: 07/28/2024] [Indexed: 08/24/2024]
Abstract
Protein glycation is a universal, non-enzymatic modification that occurs when a sugar covalently attaches to a primary amine. These spontaneous modifications may have deleterious or regulatory effects on protein function, and their removal is mediated by the conserved metabolic kinase fructosamine-3-kinase (FN3K). Despite its crucial role in protein repair, we currently have a poor understanding of how FN3K engages or phosphorylates its substrates. By integrating structural biology and biochemistry, we elucidated the catalytic mechanism for FN3K-mediated protein deglycation. Our work identifies key amino acids required for binding and phosphorylating glycated substrates and reveals the molecular basis of an evolutionarily conserved protein repair pathway. Additional structural-functional studies revealed unique structural features of human FN3K as well as differences in the dimerization behavior and regulation of FN3K family members. Our findings improve our understanding of the structure of FN3K and its catalytic mechanism, which opens new avenues for therapeutically targeting FN3K.
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Affiliation(s)
- Jameela Lokhandwala
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Jenet K Matlack
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA; Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Tracess B Smalley
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Robert E Miner
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA; Cancer Chemical Biology PhD Program, University of South Florida, Tampa, FL 33612, USA
| | - Timothy H Tran
- Chemical Biology Core, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Jennifer M Binning
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA.
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6
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Tsahnang Fofack HM, Mbah Bake M, Petry S, Ateba BA, Amoa Onguéné P, Mohammad-Salim H, Ntie-Kang F, Mbaze LM, Vakal S, Kenfack CA. Identification of potential dipeptidyl peptidase IV inhibitors from the ConMedNP library by virtual screening, and molecular dynamics methods. Heliyon 2024; 10:e35191. [PMID: 39165954 PMCID: PMC11334638 DOI: 10.1016/j.heliyon.2024.e35191] [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: 05/07/2024] [Revised: 07/06/2024] [Accepted: 07/24/2024] [Indexed: 08/22/2024] Open
Abstract
In this study, we screened novel dipeptidyl peptidase IV (DPP4) inhibitors from the ConMedNP library consisting of 3507 molecules. Interestingly, molecular docking, ADMET, and the anti-diabetic activity predictions suggest that three molecules, namely OTH_UD_XX06_1, GB19, and BMC_000104, have a high binding affinity toward DPP4. The molecular dynamics (MD) simulation results suggest that these hit molecules have a stable binding pose and occupy the binding pockets throughout the 200 ns simulation. The presence of intermolecular H-bonding between the ligands and DPP4 was observed throughout the simulation period. Thus, docking and MD results, predicted that the three compounds were the most potent DPP4 inhibitors that could putatively bind to the DPP4 active site via both conventional H-bonding and hydrophobic interactions. These results could aid the discovery of new drugs to treat type 2 diabetes.
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Affiliation(s)
- Hans Merlin Tsahnang Fofack
- Laboratoire Optique et Applications, Centre de Physique Atomique Moleculaire et Optique Quantique, Faculte des Sciences, Université de Douala, B.P. 8580, Douala, Cameroon
- Analytical, Structural and Materials Chemistry Laboratory, Department of Chemistry, Faculty of Science, University of Douala, B.P. 24157, Douala, Cameroon
| | - Maraf Mbah Bake
- Physical and Theoretical Chemistry Unit, Laboratory of applied Physical and Analytical Chemistry, Faculty of Science, University of Yaoundé I, P.O. BOX 812, Yaoundé, Cameroon
- Computational Chemistry Laboratory, Department of Chemistry, Higher Teacher Training College, University of Yaoundé I, P. O. Box 47, Yaoundé, Cameroon
| | - Simon Petry
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Takustraße 3, 14195, Berlin, Germany
| | - Baruch A. Ateba
- Laboratoire Optique et Applications, Centre de Physique Atomique Moleculaire et Optique Quantique, Faculte des Sciences, Université de Douala, B.P. 8580, Douala, Cameroon
- Analytical, Structural and Materials Chemistry Laboratory, Department of Chemistry, Faculty of Science, University of Douala, B.P. 24157, Douala, Cameroon
| | | | - Haydar Mohammad-Salim
- Department of Chemistry, Faculty of Science, University of Zakho, Zakho, Duhok, 42001, Kurdistan Region, Iraq
- Molecular Topology and Drug Design Research Unit, Department of Physical Chemistry, Pharmacy Faculty, University of Valencia, 46100, Valencia, Spain
| | - Fidele Ntie-Kang
- Center for Drug Discovery, Faculty of Science, University of Buea, P. O. Box 63, Buea, Cameroon
- Department of Chemistry, Faculty of Science, University of Buea, P. O. Box 63, Buea, Cameroon
- Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, Kurt-Mothes Strasse 3, 06120, Halle (Saale), Germany
| | - Luc Meva'a Mbaze
- Physical and Theoretical Chemistry Laboratory, Faculty of Science, University of Yaoundé I, P.O. Box 812, Yaoundé, Cameroon
| | - Serhii Vakal
- Structural Bioinformatics Lab, Faculty of Science and Engineering, Åbo Akademi University, Tuomiokirkontori 3, 20500, Turku, Finland
| | - Cyril A Kenfack
- Laboratoire Optique et Applications, Centre de Physique Atomique Moleculaire et Optique Quantique, Faculte des Sciences, Université de Douala, B.P. 8580, Douala, Cameroon
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7
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Junior DBC, Lacerda PS, de Pilla Varotti F, Leite FHA. Towards development of new antimalarial compounds through in silico and in vitro assays. Comput Biol Chem 2024; 111:108093. [PMID: 38772047 DOI: 10.1016/j.compbiolchem.2024.108093] [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: 12/18/2023] [Revised: 02/17/2024] [Accepted: 05/01/2024] [Indexed: 05/23/2024]
Abstract
Malaria is one of most widespread infectious disease in world. The antimalarial therapy presents a series of limitations, such as toxicity and the emergence of resistance, which makes the search for new drugs urgent. Thus, it becomes necessary to explore essential and exclusive therapeutic targets of the parasite to achieve selective inhibition. Enoyl-ACP reductase is an enzyme of the type II fatty acid biosynthetic pathway and is responsible for the rate-limiting step in the fatty acid elongation cycle. In this work, we use hierarchical virtual screening and drug repositioning strategies to prioritize compounds for phenotypic assays and molecular dynamics studies. The molecules were tested against chloroquine-resistant W2 strain of Plasmodium falciparum (EC50 between 330.05 and 13.92 µM). Nitrofurantoin was the best antimalarial activity at low micromolar range (EC50 = 13.92 µM). However, a hit compound against malaria must have a biological activity value below 1 µM. A large number of molecules present problems with permeability in biological membranes and reaching an effective concentration in their target's microenvironment. Nitrofurantoin derivatives with inclusions of groups which confer increased lipid solubility (methyl groups, halogens and substituted and unsubstituted aromatic rings) have been proposed. These derivatives were pulled through the lipid bilayer in molecular dynamics simulations. Molecules 14, 18 and 21 presented lower free energy values than nitrofurantoin when crossing the lipid bilayer.
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Affiliation(s)
| | - Pedro Sousa Lacerda
- Laboratório de Bioinformática e Modelagem Molecular, Universidade Federal da Bahia, Brazil
| | | | - Franco Henrique Andrade Leite
- Programa de pós-graduação em Biotecnologia, Universidade Estadual de Feira de Santana, Brazil; Programa de pós-graduação em Ciências Farmacêuticas, Universidade Estadual de Feira de Santana, Brazil; Laboratório de Modelagem Molecular, Universidade Estadual de Feira de Santana, Brazil.
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8
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Xie L, Hao X, Xie J, Mo J, Yuan C, Chen W. Acetylated pelargonidin-3- O-glucoside alleviates hepatocyte lipid deposition through activating the AMPK-mediated lysosome-autophagy pathway and redox state. Food Funct 2024; 15:6929-6942. [PMID: 38659316 DOI: 10.1039/d4fo00185k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Nonalcoholic fatty liver disease (NAFLD) is a worldwide public health issue, but a widely accepted therapy is still lacking until now. Anthocyanins are natural flavonoid compounds that possess various bioactivities, but their applications are limited due to their low bioavailability and stability. Acylated anthocyanins are reported to show higher stability, whereas their effects on NAFLD are still unclear. Herein, pelargonidin-3-O-(6''-acetyl)-glucoside (Ace Pg3G) was found to dose-dependently reduce intracellular lipid droplets and triglycerides, and improve cellular oxidative stress that accompanied lipid deposition. Besides, Ace Pg3G was proved to activate AMPK phosphorylation, thus stimulating AMPK-mediated lysosome-autophagy pathway to eliminate overloaded lipid. Further study unveiled that Ace Pg3G regulated genes related to lipid metabolism downstream of AMPK to inhibit lipid synthesis and accelerate lipid oxidation. Overall, this study provided the first evidence, to our best knowledge, that Ace Pg3G ameliorated free fatty acid-induced lipid deposition in hepatocytes through regulating AMPK-mediated autophagy pathways and redox state.
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Affiliation(s)
- Lianghua Xie
- Department of Traditional Chinese Medicine, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310016, China.
- Department of Food Science and Nutrition, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Xin Hao
- Department of Food Science and Nutrition, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Jiahong Xie
- Department of Food Science and Nutrition, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Jianling Mo
- Department of Traditional Chinese Medicine, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310016, China.
| | - Changzheng Yuan
- School of Public Health, Zhejiang University School of Medicine, Hangzhou, 310058, China.
| | - Wei Chen
- Department of Traditional Chinese Medicine, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310016, China.
- Department of Food Science and Nutrition, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
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9
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Chompunud Na Ayudhya C, Graidist P, Tipmanee V. Role of CSF1R 550th-tryptophan in kusunokinin and CSF1R inhibitor binding and ligand-induced structural effect. Sci Rep 2024; 14:12531. [PMID: 38822100 PMCID: PMC11143223 DOI: 10.1038/s41598-024-63505-x] [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: 03/05/2024] [Accepted: 05/29/2024] [Indexed: 06/02/2024] Open
Abstract
Binding affinity is an important factor in drug design to improve drug-target selectivity and specificity. In this study, in silico techniques based on molecular docking followed by molecular dynamics (MD) simulations were utilized to identify the key residue(s) for CSF1R binding affinity among 14 pan-tyrosine kinase inhibitors and 15 CSF1R-specific inhibitors. We found tryptophan at position 550 (W550) on the CSF1R binding site interacted with the inhibitors' aromatic ring in a π-π way that made the ligands better at binding. Upon W550-Alanine substitution (W550A), the binding affinity of trans-(-)-kusunokinin and imatinib to CSF1R was significantly decreased. However, in terms of structural features, W550 did not significantly affect overall CSF1R structure, but provided destabilizing effect upon mutation. The W550A also did not either cause ligand to change its binding site or conformational changes due to ligand binding. As a result of our findings, the π-π interaction with W550's aromatic ring could be still the choice for increasing binding affinity to CSF1R. Nevertheless, our study showed that the increasing binding to W550 of the design ligand may not ensure CSF1R specificity and inhibition since W550-ligand bound state did not induce significantly conformational change into inactive state.
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Affiliation(s)
- Chompunud Chompunud Na Ayudhya
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Hat Yai, 90100, Songkhla, Thailand
| | - Potchanapond Graidist
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Hat Yai, 90100, Songkhla, Thailand
- Bioactivity Testing Center, Faculty of Medicine, Prince of Songkla University, Hat Yai, 90100, Songkhla, Thailand
| | - Varomyalin Tipmanee
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Hat Yai, 90100, Songkhla, Thailand.
- Bioactivity Testing Center, Faculty of Medicine, Prince of Songkla University, Hat Yai, 90100, Songkhla, Thailand.
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10
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Holmes J, Islam SM, Milligan KA. Exploring Cannabinoids as Potential Inhibitors of SARS-CoV-2 Papain-like Protease: Insights from Computational Analysis and Molecular Dynamics Simulations. Viruses 2024; 16:878. [PMID: 38932170 PMCID: PMC11209085 DOI: 10.3390/v16060878] [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: 04/06/2024] [Revised: 05/21/2024] [Accepted: 05/27/2024] [Indexed: 06/28/2024] Open
Abstract
The emergence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has triggered a global COVID-19 pandemic, challenging healthcare systems worldwide. Effective therapeutic strategies against this novel coronavirus remain limited, underscoring the urgent need for innovative approaches. The present research investigates the potential of cannabis compounds as therapeutic agents against SARS-CoV-2 through their interaction with the virus's papain-like protease (PLpro) protein, a crucial element in viral replication and immune evasion. Computational methods, including molecular docking and molecular dynamics (MD) simulations, were employed to screen cannabis compounds against PLpro and analyze their binding mechanisms and interaction patterns. The results showed cannabinoids with binding affinities ranging from -6.1 kcal/mol to -4.6 kcal/mol, forming interactions with PLpro. Notably, Cannabigerolic and Cannabidiolic acids exhibited strong binding contacts with critical residues in PLpro's active region, indicating their potential as viral replication inhibitors. MD simulations revealed the dynamic behavior of cannabinoid-PLpro complexes, highlighting stable binding conformations and conformational changes over time. These findings shed light on the mechanisms underlying cannabis interaction with SARS-CoV-2 PLpro, aiding in the rational design of antiviral therapies. Future research will focus on experimental validation, optimizing binding affinity and selectivity, and preclinical assessments to develop effective treatments against COVID-19.
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Affiliation(s)
| | - Shahidul M. Islam
- Department of Chemistry, Delaware State University, 1200 N. DuPont Hwy, Dover, DE 19901, USA; (J.H.); (K.A.M.)
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Zhang X, Zhou L, Qian X. The Mechanism of "Treating Different Diseases with the Same Treatment" by Qiangji Jianpi Decoction in Ankylosing Spondylitis Combined with Inflammatory Bowel Disease: A Comprehensive Analysis of Multiple Methods. Gastroenterol Res Pract 2024; 2024:9709260. [PMID: 38808131 PMCID: PMC11132832 DOI: 10.1155/2024/9709260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 04/17/2024] [Accepted: 05/07/2024] [Indexed: 05/30/2024] Open
Abstract
Background Ankylosing spondylitis (AS) and inflammatory bowel disease (IBD) are prevalent autoimmune disorders that often co-occur, posing significant treatment challenges. This investigation adopts a multidisciplinary strategy, integrating bioinformatics, network pharmacology, molecular docking, and Mendelian randomization, to elucidate the relationship between AS and IBD and to investigate the potential mechanisms of traditional Chinese medicine formulations, represented by Qiangji Jianpi (QJJP) decoction, in treating these comorbid conditions. Methods We utilized databases to pinpoint common targets among AS, IBD, and QJJP decoction's active compounds through intersection analysis. Through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses, we mapped a network in Cytoscape, isolating critical targets. Molecular docking with AutoDock validated the affinity between targets and compounds. ROC analysis and dataset validation assessed diagnostic performance, while Gene Set Enrichment Analysis (GSEA) offered pathway insights. Mendelian randomization explored the AS-IBD causal relationship. Results Screening identified 105 targets for QJJP decoction, 414 for AS, and 2420 for IBD, with 85 overlapping. These targets predominantly participate in organismal responses and DNA transcription factor binding, with a significant cellular presence in the endoplasmic reticulum and vesicle lumen. Molecular docking, facilitated by Cytoscape, confirmed IL1A, IFNG, TGFB1, and EDN1 as critical targets, with IFNG demonstrating diagnostic potential through GEO dataset validation. The integration of GSEA with network pharmacology highlighted the therapeutic significance of the relaxin, osteoclast differentiation, HIF-1, and AGE-RAGE signaling pathways in QJJP decoction's action. Mendelian randomization analysis indicated a positive causal relationship between IBD and AS, pinpointing rs2193041 as a key SNP influencing IFNG. Conclusion Based on the principle of "treating different diseases with the same method" in traditional Chinese medicine theory, we explored the intricate mechanisms through which QJJP decoction addresses AS and IBD comorbidity. Our research spotlighted the pivotal role of the IFNG gene. IFNG emerges not only as a key therapeutic target but also assumes significance as a potential diagnostic biomarker through its genetic underpinnings. This investigation establishes a solid base for subsequent experimental inquiries. Our findings introduce novel approaches for incorporating traditional Chinese medicine into the treatment of AS-IBD comorbidity, setting the stage for groundbreaking research directions.
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Affiliation(s)
- Xuhong Zhang
- Wuxi Affiliated Hospital of Nanjing University of Chinese Medicine, Wuxi, China
| | - Lamei Zhou
- Wuxi Affiliated Hospital of Nanjing University of Chinese Medicine, Wuxi, China
| | - Xian Qian
- Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
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12
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Douglas JT, Johnson DK, Roy A, Park T. Use of phosphotyrosine-containing peptides to target SH2 domains: Antagonist peptides of the Crk/CrkL-p130Cas axis. Methods Enzymol 2024; 698:301-342. [PMID: 38886037 DOI: 10.1016/bs.mie.2024.04.013] [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] [Indexed: 06/20/2024]
Abstract
Protein-protein interactions between SH2 domains and segments of proteins that include a post-translationally phosphorylated tyrosine residue (pY) underpin numerous signal transduction cascades that allow cells to respond to their environment. Dysregulation of the writing, erasing, and reading of these posttranslational modifications is a hallmark of human disease, notably cancer. Elucidating the precise role of the SH2 domain-containing adaptor proteins Crk and CrkL in tumor cell migration and invasion is challenging because there are no specific and potent antagonists available. Crk and CrkL SH2s interact with a region of the docking protein p130Cas containing 15 potential pY-containing tetrapeptide motifs. This chapter summarizes recent efforts toward peptide antagonists for this Crk/CrkL-p130Cas interaction. We describe our protocol for recombinant expression and purification of Crk and CrkL SH2s for functional assays and our procedure to determine the consensus binding motif from the p130Cas sequence. To develop a more potent antagonist, we employ methods often associated with structure-based drug design. Computational docking using Rosetta FlexPepDock, which accounts for peptides having a greater number of conformational degrees of freedom than small organic molecules that typically constitute libraries, provides quantitative docking metrics to prioritize candidate peptides for experimental testing. A battery of biophysical assays, including fluorescence polarization, differential scanning fluorimetry and saturation transfer difference nuclear magnetic resonance spectroscopy, were employed to assess the candidates. In parallel, GST pulldown competition assays characterized protein-protein binding in vitro. Taken together, our methodology yields peptide antagonists of the Crk/CrkL-p130Cas axis that will be used to validate targets, assess druggability, foster in vitro assay development, and potentially serve as lead compounds for therapeutic intervention.
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Affiliation(s)
- Justin T Douglas
- Nuclear Magnetic Resonance Core Lab, University of Kansas, Lawrence, KS, United States
| | - David K Johnson
- Computational Chemical Biology Core, Molecular Graphics and Modeling Laboratory, University of Kansas, Lawrence, Kansas, United States
| | - Anuradha Roy
- High Throughput Screening Laboratory, University of Kansas, Lawrence, KS, United States
| | - Taeju Park
- Department of Pediatrics, Children's Mercy Kansas City and University of Missouri Kansas City School of Medicine, Kansas City, MO, United States
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Rabaan AA, Alshahrani FS, Garout M, Alissa M, Mashraqi MM, Alshehri AA, Alsaleh AA, Alwarthan S, Sabour AA, Alfaraj AH, AlShehail BM, Alotaibi N, Abduljabbar WA, Aljeldah M, Alestad JH. Repositioning of anti-infective compounds against monkeypox virus core cysteine proteinase: a molecular dynamics study. Mol Divers 2024:10.1007/s11030-023-10802-8. [PMID: 38652365 DOI: 10.1007/s11030-023-10802-8] [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: 07/12/2023] [Accepted: 12/26/2023] [Indexed: 04/25/2024]
Abstract
Monkeypox virus (MPXV) core cysteine proteinase (CCP) is one of the major drug targets used to examine the inhibitory action of chemical moieties. In this study, an in silico technique was applied to screen 1395 anti-infective compounds to find out the potential molecules against the MPXV-CCP. The top five hits were selected after screening and processed for exhaustive docking based on the docked score of ≤ -9.5 kcal/mol. Later, the top three hits based on the exhaustive-docking score and interaction profile were selected to perform MD simulations. The overall RMSD suggested that two compounds, SC75741 and ammonium glycyrrhizinate, showed a highly stable complex with a standard deviation of 0.18 and 0.23 nm, respectively. Later, the MM/GBSA binding free energies of complexes showed significant binding strength with ΔGTOTAL from -21.59 to -15 kcal/mol. This report reported the potential inhibitory activity of SC75741 and ammonium glycyrrhizinate against MPXV-CCP by competitively inhibiting the binding of the native substrate.
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Affiliation(s)
- Ali A Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, 31311, Dhahran, Saudi Arabia.
- College of Medicine, Alfaisal University, 11533, Riyadh, Saudi Arabia.
- Department of Public Health and Nutrition, The University of Haripur, Haripur, 22610, Pakistan.
| | - Fatimah S Alshahrani
- Department of Internal Medicine, College of Medicine, King Saud University, 11362, Riyadh, Saudi Arabia
- Division of Infectious Diseases, Department of Internal Medicine, College of Medicine, King Saud University and King Saud University Medical City, 11451, Riyadh, Saudi Arabia
| | - Mohammed Garout
- Department of Community Medicine and Health Care for Pilgrims, Faculty of Medicine, Umm Al-Qura University, 21955, Makkah, Saudi Arabia
| | - Mohammed Alissa
- Department of Medical Laboratory, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, 11942, Al-Kharj, Saudi Arabia
| | - Mutaib M Mashraqi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, 61441, Najra, Saudi Arabia
| | - Ahmad A Alshehri
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, 61441, Najra, Saudi Arabia
| | - Abdulmonem A Alsaleh
- Clinical Laboratory Science Department, Mohammed Al-Mana College for Medical Sciences, 34222, Dammam, Saudi Arabia
| | - Sara Alwarthan
- Department of Internal Medicine, College of Medicine, Imam Abdulrahman Bin Faisal University, 34212, Dammam, Saudi Arabia
| | - Amal A Sabour
- Department of Botany and Microbiology, College of Science, King Saud University, 11451, Riyadh, Saudi Arabia
| | - Amal H Alfaraj
- Pediatric Department, Abqaiq General Hospital, First Eastern Health Cluster, 33261, Abqaiq, Saudi Arabia
| | - Bashayer M AlShehail
- Pharmacy Practice Department, College of Clinical Pharmacy, Imam Abdulrahman Bin Faisal University, 31441, Dammam, Saudi Arabia
| | - Nouf Alotaibi
- Clinical pharmacy Department, College of Pharmacy, Umm Al-Qura University, 21955, Makkah, Saudi Arabia
| | - Wesam A Abduljabbar
- Department of Medical laboratory sciences, Fakeeh College for Medical Science, 21134, Jeddah, Saudi Arabia
| | - Mohammed Aljeldah
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hafr Al Batin, 39831, Hafr Al Batin, Saudi Arabia
| | - Jeehan H Alestad
- Immunology and Infectious Microbiology Department, University of Glasgow, Glasgow, G1 1XQ, UK.
- Microbiology Department, Collage of Medicine, 46300, Jabriya, Kuwait.
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Muhammad S, Zahir N, Bibi S, Alshahrani MY, Shafiq-urRehman, Chaudhry AR, Sarwar F, Tousif MI. Computational prediction for designing novel ketonic derivatives as potential inhibitors for breast cancer: A trade-off between drug likeness and inhibition potency. Comput Biol Chem 2024; 109:108020. [PMID: 38286082 DOI: 10.1016/j.compbiolchem.2024.108020] [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: 08/24/2023] [Revised: 01/10/2024] [Accepted: 01/11/2024] [Indexed: 01/31/2024]
Abstract
Unlike simple molecular screening, a combined hybrid computational methodology has been applied which includes quantum chemical methods, molecular docking, and molecular dynamics simulations to design some novel ketonic derivatives. The current study contains the derivatives of an experimental ligand which are designed as a trade-off between drug likeness and inhibition strength. We investigate the interaction of various newly designed ketonic compounds with the breast cancer receptor known as the Estrogen Receptor Alpha (ERα). The molecular structures of all newly designed ligands were studied quantum chemically in terms of their fully optimized structures, 3-D molecular orbital distributions, global chemical descriptors, molecular electrostatic potentials and energies of frontier molecular orbitals (FMOs). All ligands under study show good binding affinities with the ERα protein. The ligands CMR2 and CMR4 exhibit improved molecular docking interactions. The intermolecular interactions indicate that CMR4 demonstrates better hydrophobic and hydrogen bonding interactions with protein (ERα). Furthermore, molecular dynamics simulations were conducted on ligands and reference drugs interacting with the ERα protein over a time span of 120 nanoseconds. The molecular dynamics results are interpreted in terms of ligand-protein stability and flexible behaviour based on their respective values of RMSD, RMSF, H-bonds, the radius of gyration, and SASA graphs. To analyse ligand-protein interactions throughout the entire 120 ns trajectory, a more advanced MM/PBSA method is utilized, where six selected ligands (CMR1, CMR2, CMR3, CMR4, CMR5 and CMR9) illustrate promising results for inhibition of the ERα receptor as assessed through MM/BBSA analysis. The CMR9 has the highest MM/BBSA binding free energy (-14.46 kcal/mol). The ADMET analysis reveals that CMR4 has maximum intestinal absorption (6.68) and clearance rate (0.1). All the compounds are non-toxic and safe to use. These findings indicate the potential of involving different computational techniques to design the ligand structures and to study the ligand-protein interactions for better understanding and achieving more potent synthetic inhibitors for breast cancer.
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Affiliation(s)
- Shabbir Muhammad
- Department of Chemistry, College of Science, King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia.
| | - Nimra Zahir
- Department of Chemistry, University of Agriculture, Faisalabad 38000, Pakistan
| | - Shamsa Bibi
- Department of Chemistry, University of Agriculture, Faisalabad 38000, Pakistan.
| | - Mohammad Y Alshahrani
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, P.O. Box 61413, Abha 9088, Saudi Arabia
| | - Shafiq-urRehman
- Department of Chemistry, University of Agriculture, Faisalabad 38000, Pakistan
| | - Aijaz Rasool Chaudhry
- Department of Physics, College of Science, University of Bisha, P.O. Box 551, Bisha 61922, Saudi Arabia
| | - Fatima Sarwar
- Department of Chemistry, University of Agriculture, Faisalabad 38000, Pakistan
| | - Muhammad Imran Tousif
- Department of Chemistry, Division of Science and Technology, University of Education, Lahore 54770, Pakistan
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Bernacchia L, Paris A, Gupta A, Charman RJ, McGreig J, Wass MN, Kad NM. Identification of a novel DNA repair inhibitor using an in silico driven approach shows effective combinatorial activity with genotoxic agents against multidrug-resistant Escherichia coli. Protein Sci 2024; 33:e4948. [PMID: 38501485 PMCID: PMC10949335 DOI: 10.1002/pro.4948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 01/30/2024] [Accepted: 02/12/2024] [Indexed: 03/20/2024]
Abstract
Increasing antimicrobial drug resistance represents a global existential threat. Infection is a particular problem in immunocompromised individuals, such as patients undergoing cancer chemotherapy, due to the targeting of rapidly dividing cells by antineoplastic agents. We recently developed a strategy that targets bacterial nucleotide excision DNA repair (NER) to identify compounds that act as antimicrobial sensitizers specific for patients undergoing cancer chemotherapy. Building on this, we performed a virtual drug screening of a ~120,000 compound library against the key NER protein UvrA. From this, numerous target compounds were identified and of those a candidate compound, Bemcentinib (R428), showed a strong affinity toward UvrA. This NER protein possesses four ATPase sites in its dimeric state, and we found that Bemcentinib could inhibit UvrA's ATPase activity by ~90% and also impair its ability to bind DNA. As a result, Bemcentinib strongly diminishes NER's ability to repair DNA in vitro. To provide a measure of in vivo activity we discovered that the growth of Escherichia coli MG1655 was significantly inhibited when Bemcentinib was combined with the DNA damaging agent 4-NQO, which is analogous to UV. Using the clinically relevant DNA-damaging antineoplastic cisplatin in combination with Bemcentinib against the urological sepsis-causing E. coli strain EC958 caused complete growth inhibition. This study offers a novel approach for the potential development of new compounds for use as adjuvants in antineoplastic therapy.
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Affiliation(s)
| | - Antoine Paris
- School of Biological SciencesUniversity of KentCanterburyUK
| | - Arya Gupta
- School of Biological SciencesUniversity of KentCanterburyUK
| | | | - Jake McGreig
- School of Biological SciencesUniversity of KentCanterburyUK
| | - Mark N. Wass
- School of Biological SciencesUniversity of KentCanterburyUK
| | - Neil M. Kad
- School of Biological SciencesUniversity of KentCanterburyUK
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16
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Weller JA, Rohs R. DrugHIVE: Target-specific spatial drug design and optimization with a hierarchical generative model. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.22.573155. [PMID: 38187658 PMCID: PMC10769420 DOI: 10.1101/2023.12.22.573155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Rapid advancement in the computational methods of structure-based drug design has led to their widespread adoption as key tools in the early drug development process. Recently, the remarkable growth of available crystal structure data and libraries of commercially available or readily synthesizable molecules have unlocked previously inaccessible regions of chemical space for drug development. Paired with improvements in virtual ligand screening methods, these expanded libraries are having a significant impact on the success of early drug design efforts. However, screening-based methods are limited in their scalability due to computational limits and the sheer scale of drug-like space. An approach within the quickly evolving field of artificial intelligence (AI), deep generative modeling, is extending the reach of molecular design beyond classical methods by learning the fundamental intra- and inter-molecular relationships in drug-target systems from existing data. In this work we introduce DrugHIVE, a deep hierarchical structure-based generative model that enables fine-grained control over molecular generation. Our model outperforms state of the art autoregressive and diffusion-based methods on common benchmarks and in speed of generation. Here, we demonstrate DrugHIVEs capacity to accelerate a wide range of common drug design tasks such as de novo generation, molecular optimization, scaffold hopping, linker design, and high throughput pattern replacement. Our method is highly scalable and can be applied to high confidence AlphaFold predicted receptors, extending our ability to generate high quality drug-like molecules to a majority of the unsolved human proteome.
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Kumar S, Ali I, Abbas F, Shafiq F, Yadav AK, Ghate MD, Kumar D. In-silico identification and exploration of small molecule coumarin-1,2,3-triazole hybrids as potential EGFR inhibitors for targeting lung cancer. Mol Divers 2024:10.1007/s11030-024-10817-9. [PMID: 38470555 DOI: 10.1007/s11030-024-10817-9] [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: 08/14/2023] [Accepted: 01/25/2024] [Indexed: 03/14/2024]
Abstract
Globally, lung cancer is a significant public health concern due to its role as the leading cause of cancer-related mortalities. The promising target of EGFR for lung cancer treatment has been identified, providing a potential avenue for more effective therapies. The purpose of the study was to design a library of 1843 coumarin-1,2,3-triazole hybrids and screen them based on a designed pharmacophore to identify potential inhibitors targeting EGFR in lung cancer with minimum or no side effects. Pharmacophore-based screening was carried out and 60 hits were obtained. To gain a better understanding of the binding interactions between the compounds and the targeted receptor, molecular docking was conducted on the 60 screened compounds. In-silico ADME and toxicity studies were also conducted to assess the drug-likeness and safety of the identified compounds. The results indicated that coumarin-1,2,3-triazole hybrids COUM-0849, COUM-0935, COUM-0414, COUM-1335, COUM-0276, and COUM-0484 exhibit dock score of - 10.2, - 10.2, - 10.1, - 10.1, - 10, - 10 while reference molecule - 7.9 kcal/mol for EGFR (PDB ID: 4HJO) respectively. The molecular docking and molecular dynamics simulations revealed that the identified compounds formed stable interactions with the active site of EGFR, indicating their potential as inhibitors. The in-silico ADME and toxicity studies showed that the compounds had favorable drug-likeness properties and low toxicity, further supporting their potential as therapeutic agents. Finally, we performed DFT studies on the best-selected ligands to gain further insights into their electronic properties. The findings of this study provide important insights into the potential of coumarin-1,2,3-triazole hybrids as promising EGFR inhibitors for the management of lung cancer.
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Affiliation(s)
- Sunil Kumar
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Shoolini University, Solan, Himachal Pradesh, 173229, India
| | - Iqra Ali
- Department of Biosciences, COMSATS University Islamabad, Islamabad Campus, Islamabad, 45550, Pakistan
| | - Faheem Abbas
- Key Lab of Organic Optoelectronics and Molecular Engineering of Ministry of Education, Department of Chemistry, Tsinghua University, Beijing, 100084, People's Republic of China
| | - Faiza Shafiq
- Department of Chemistry, University of Agriculture, Faisalabad, 38040, Pakistan
| | - Ashok Kumar Yadav
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh, 160014, India
| | - Manjunath D Ghate
- School of Pharmacy, National Forensic Sciences University, Gandhinagar, Gujarat, 382007, India
| | - Deepak Kumar
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Shoolini University, Solan, Himachal Pradesh, 173229, India.
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Ma B, Shi S, Guo W, Zhang H, Zhao Z, An H. Liensinine, a Novel and Food-Derived Compound, Exerts Potent Antihepatoma Efficacy via Inhibiting the Kv10.1 Channel. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:4689-4702. [PMID: 38382537 DOI: 10.1021/acs.jafc.3c06142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Plant metabolites from natural product extracts offer unique advantages against carcinogenesis in the development of drugs. The target-based virtual screening from food-derived compounds represents a promising approach for tumor therapy. In this study, we performed virtual screening to target the presumed inhibitor-binding pocket and identified a highly potent Kv10.1 inhibitor, liensinine (Lien), which can inhibit the channel in a dose-dependent way with an IC50 of 0.24 ± 0.07 μM. Combining molecular dynamics simulations with mutagenesis experiments, our data show that Lien interacts with Kv10.1 by binding with Y539, T543, D551, E553, and H601 in the C-linker domain of Kv10.1. In addition, the interaction of sequence alignment and 3D structural modeling revealed differences between the C-linker domain of the Kv10.1 channel and the Kv11.1 channel. Furthermore, antitumor experiments revealed that Lien suppresses the proliferation and migration of HCC both in vitro and in vivo. In summary, the food-derived compound, Lien, may serve as a lead compound for antihepatoma therapeutic drugs targeting Kv10.1.
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Affiliation(s)
- Biao Ma
- State Key Laboratory of Reliability and Intelligence of Electrical Equipment, Hebei University of Technology, Tianjin 300401, China
- Key Laboratory of Electromagnetic Field and Electrical Apparatus Reliability of Hebei Province, Hebei University of Technology, Tianjin 300401, China
- Key Laboratory of Molecular Biophysics, Hebei Province, Institute of Biophysics, School of Health Sciences & Biomedical Engineering, Hebei University of Technology, Tianjin 300401, China
| | - Sai Shi
- Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin 300072, China
| | - Wei Guo
- Key Laboratory of Molecular Biophysics, Hebei Province, Institute of Biophysics, School of Health Sciences & Biomedical Engineering, Hebei University of Technology, Tianjin 300401, China
| | - Hailin Zhang
- Department of Pharmacology, Hebei Medical University, Shijiazhuang 050017, China
| | - Zhen Zhao
- Key Laboratory of Molecular Biophysics, Hebei Province, Institute of Biophysics, School of Health Sciences & Biomedical Engineering, Hebei University of Technology, Tianjin 300401, China
| | - Hailong An
- State Key Laboratory of Reliability and Intelligence of Electrical Equipment, Hebei University of Technology, Tianjin 300401, China
- Key Laboratory of Electromagnetic Field and Electrical Apparatus Reliability of Hebei Province, Hebei University of Technology, Tianjin 300401, China
- Key Laboratory of Molecular Biophysics, Hebei Province, Institute of Biophysics, School of Health Sciences & Biomedical Engineering, Hebei University of Technology, Tianjin 300401, China
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Szlapa-Kula A, Kula S, Kaźmierski Ł, Biernasiuk A, Krawczyk P. Can a Small Change in the Heterocyclic Substituent Significantly Impact the Physicochemical and Biological Properties of ( Z)-2-(5-Benzylidene-4-oxo-2-thioxothiazolidin-3-yl)acetic Acid Derivatives? SENSORS (BASEL, SWITZERLAND) 2024; 24:1524. [PMID: 38475060 DOI: 10.3390/s24051524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 02/05/2024] [Accepted: 02/19/2024] [Indexed: 03/14/2024]
Abstract
Rhodanine-3-acetic acid derivatives are attractive compounds with versatile effects. What is very important is that compounds of this type have many biological properties. They are tested, among others, as fluorescent probes for bioimaging and aldose reductase inhibitors. Rhodanine-3-acetic acid derivatives also have antibacterial, antifungal and anticancer activity. The presented work demonstrates that a slight change in the five-membered heterocyclic substituent significantly affects the properties of the compounds under consideration. Three rhodanine-3-acetic acid derivatives (A-1-A-3) were obtained in the Knoevenagel condensation reaction with good yields, ranging from 54% to 71%. High thermal stability of the tested compounds was also demonstrated above 240 °C. The absorption and emission maxima in polar and non-polar solvents were determined. Then, the possibility of using the considered derivatives for fluorescence bioimaging was checked. Compounds A-1 and A-2 were successfully used as fluorescent dyes of fixed cells of mammalian origin. In addition, biological activity tests against bacteria and fungi were carried out. Our results showed that A-1 and A-2 showed the most excellent antimicrobial activity among the newly synthesized compounds, especially against Gram-positive bacteria.
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Affiliation(s)
- Agata Szlapa-Kula
- Institute of Chemistry, Faculty of Science and Technology, University of Silesia in Katowice, Szkolna 9 St., 40-007 Katowice, Poland
| | - Slawomir Kula
- Institute of Chemistry, Faculty of Science and Technology, University of Silesia in Katowice, Szkolna 9 St., 40-007 Katowice, Poland
| | - Łukasz Kaźmierski
- Urology and Andrology, Department of Tissue Engineering, Collegium Medicum, Nicolaus Copernicus University, M. Curie Skłodowskiej 9, 85-094 Bydgoszcz, Poland
| | - Anna Biernasiuk
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Medical University of Lublin, 20-093 Lublin, Poland
| | - Przemysław Krawczyk
- Department of Physical Chemistry, Faculty of Pharmacy, Collegium Medicum, Nicolaus Copernicus University, Kurpińskiego 5, 85-950 Bydgoszcz, Poland
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Governa P, Biagi M, Manetti F, Forli S. Consensus screening for a challenging target: the quest for P-glycoprotein inhibitors. RSC Med Chem 2024; 15:720-732. [PMID: 38389870 PMCID: PMC10880898 DOI: 10.1039/d3md00649b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 01/18/2024] [Indexed: 02/24/2024] Open
Abstract
ATP-binding cassette (ABC) transporters are a large family of proteins involved in membrane transport of a wide variety of substrates. Among them, ABCB1, also known as MDR-1 or P-glycoprotein (P-gp), is the most characterized. By exporting xenobiotics out of the cell, P-gp activity can affect the ADME properties of several drugs. Moreover, P-gp has been found to mediate multidrug resistance in cancer cells. Thus, the inhibition of P-gp activity may lead to increased absorption and/or intracellular accumulation of co-administered drugs, enhancing their effectiveness. Using the human-mouse chimeric cryoEM 3D structure of the P-gp in the inhibitor-bound intermediate form (PDBID: 6qee), approximately 200 000 commercially available natural compounds from the ZINC database were virtually screened. To build a model able to discriminate between substrate and inhibitors, two datasets of compounds with known activity, including P-gp inhibitors, substrates, and inactive molecules were also docked. The best docking pose of selected substrates and inhibitors were used to generate 3D common feature pharmacophoric models that were combined with the Autodock Vina binding energy values to prioritize compounds for visual inspection. With this consensus approach, 13 potential candidates were identified and then tested for their ability to inhibit P-gp, using zosuquidar, a third generation P-gp inhibitor, as a reference drug. Eight compounds were found to be active with 6 of them having an IC50 lower than 5 μM in a membrane-based ATPase activity assay. Moreover, the P-gp inhibitory activity was also confirmed by two different cell-based in vitro methods. Both retrospective and prospective results demonstrate the ability of the combined structure-based pharmacophore modeling and docking-based virtual screening approach to predict novel hit compounds with inhibitory activity toward P-gp. The resulting chemical scaffolds could serve as inspiration for the optimization of novel and more potent P-gp inhibitors.
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Affiliation(s)
- Paolo Governa
- Department of Integrative Structural and Computational Biology, Scripps Research Institute La Jolla CA 92037 USA
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena 53100 Siena Italy
| | - Marco Biagi
- Department of Food and Drug, University of Parma 43121 Parma Italy
| | - Fabrizio Manetti
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena 53100 Siena Italy
| | - Stefano Forli
- Department of Integrative Structural and Computational Biology, Scripps Research Institute La Jolla CA 92037 USA
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Elbouzidi A, Taibi M, Laaraj S, Loukili EH, Haddou M, El Hachlafi N, Naceiri Mrabti H, Baraich A, Bellaouchi R, Asehraou A, Bourhia M, Nafidi HA, Bin Jardan YA, Chaabane K, Addi M. Chemical profiling of volatile compounds of the essential oil of grey-leaved rockrose ( Cistus albidus L.) and its antioxidant, anti-inflammatory, antibacterial, antifungal, and anticancer activity in vitro and in silico. Front Chem 2024; 12:1334028. [PMID: 38435667 PMCID: PMC10905769 DOI: 10.3389/fchem.2024.1334028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 01/29/2024] [Indexed: 03/05/2024] Open
Abstract
Cistus albidus: L., also known as Grey-leaved rockrose and locally addressed as šṭab or tûzzâla lbîḍa, is a plant species with a well-established reputation for its health-promoting properties and traditional use for the treatment of various diseases. This research delves into exploring the essential oil extracted from the aerial components of Cistus albidus (referred to as CAEO), aiming to comprehend its properties concerning antioxidation, anti-inflammation, antimicrobial efficacy, and cytotoxicity. Firstly, a comprehensive analysis of CAEO's chemical composition was performed through Gas Chromatography-Mass Spectrometry (GC-MS). Subsequently, four complementary assays were conducted to assess its antioxidant potential, including DPPH scavenging, β-carotene bleaching, ABTS scavenging, and total antioxidant capacity assays. The investigation delved into the anti-inflammatory properties via the 5-lipoxygenase assay and the antimicrobial effects of CAEO against various bacterial and fungal strains. Additionally, the research investigated the cytotoxic effects of CAEO on two human breast cancer subtypes, namely, MCF-7 and MDA-MB-231. Chemical analysis revealed camphene as the major compound, comprising 39.21% of the composition, followed by α-pinene (19.01%), bornyl acetate (18.32%), tricyclene (6.86%), and melonal (5.44%). Notably, CAEO exhibited robust antioxidant activity, as demonstrated by the low IC50 values in DPPH (153.92 ± 4.30 μg/mL) and β-carotene (95.25 ± 3.75 μg/mL) assays, indicating its ability to counteract oxidative damage. The ABTS assay and the total antioxidant capacity assay also confirmed the potent antioxidant potential with IC50 values of 120.51 ± 3.33 TE μmol/mL and 458.25 ± 3.67 µg AAE/mg, respectively. In terms of anti-inflammatory activity, CAEO displayed a substantial lipoxygenase inhibition at 0.5 mg/mL. Its antimicrobial properties were broad-spectrum, although some resistance was observed in the case of Escherichia coli and Staphylococcus aureus. CAEO exhibited significant dose-dependent inhibitory effects on tumor cell lines in vitro. Additionally, computational analyses were carried out to appraise the physicochemical characteristics, drug-likeness, and pharmacokinetic properties of CAEO's constituent molecules, while the toxicity was assessed using the Protox II web server.
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Affiliation(s)
- Amine Elbouzidi
- Laboratoire d’Amélioration des Productions Agricoles, Biotechnologie et Environnement (LAPABE), Faculté des Sciences, Université Mohammed Premier, Oujda, Morocco
- Euro-Mediterranean University of Fes (UEMF), Fes, Morocco
| | - Mohamed Taibi
- Laboratoire d’Amélioration des Productions Agricoles, Biotechnologie et Environnement (LAPABE), Faculté des Sciences, Université Mohammed Premier, Oujda, Morocco
- Centre de l’Oriental des Sciences et Technologies de l’Eau et de l’Environnement (COSTEE), Université Mohammed Premier, Oujda, Morocco
| | - Salah Laaraj
- Regional Center of Agricultural Research of Tadla, National Institute of Agricultural Research (INRA), Rabat, Morocco
| | | | - Mounir Haddou
- Laboratoire d’Amélioration des Productions Agricoles, Biotechnologie et Environnement (LAPABE), Faculté des Sciences, Université Mohammed Premier, Oujda, Morocco
| | - Naoufal El Hachlafi
- Laboratory of Microbial Biotechnology and Bioactive Molecules, Faculty of Sciences and Technologies Faculty, Sidi Mohamed Ben Abdellah University, Fes, Morocco
| | - Hanae Naceiri Mrabti
- High Institute of Nursing Professions and Health Techniques, Casablanca, Morocco
| | - Abdellah Baraich
- Laboratory of Bioresources, Biotechnology, Ethnopharmacology and Health, Faculty of Sciences, Mohammed First University, Oujda, Morocco
| | - Reda Bellaouchi
- Laboratory of Bioresources, Biotechnology, Ethnopharmacology and Health, Faculty of Sciences, Mohammed First University, Oujda, Morocco
| | - Abdeslam Asehraou
- Laboratory of Bioresources, Biotechnology, Ethnopharmacology and Health, Faculty of Sciences, Mohammed First University, Oujda, Morocco
| | - Mohammed Bourhia
- Laboratory of Biotechnology and Natural Resources Valorization, Faculty of Sciences of Agadir, Ibnou Zohr University, Agadir, Morocco
| | - Hiba-Allah Nafidi
- Department of Food Science, Faculty of Agricultural and Food Sciences, Laval University, Quebec City, QC, Canada
| | - Yousef A. Bin Jardan
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Khalid Chaabane
- Laboratoire d’Amélioration des Productions Agricoles, Biotechnologie et Environnement (LAPABE), Faculté des Sciences, Université Mohammed Premier, Oujda, Morocco
| | - Mohamed Addi
- Laboratoire d’Amélioration des Productions Agricoles, Biotechnologie et Environnement (LAPABE), Faculté des Sciences, Université Mohammed Premier, Oujda, Morocco
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Algaissi A, Khan E, Tabassum H, Samreen S, Khamjan NA, Lohani M, Khan S, Kameli N, Madkhali F, Ahmad IZ. Campesterol and dithymoquinone as a potent inhibitors of SARS cov-2 main proteases-promising drug candidates for targeting its novel variants. J Biomol Struct Dyn 2024:1-15. [PMID: 38288958 DOI: 10.1080/07391102.2023.2301684] [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: 02/06/2023] [Accepted: 09/13/2023] [Indexed: 02/16/2024]
Abstract
The sudden outbreak of the COVID-19 pandemic has currently taken approximately 2.4 million lives, with no specific medication and fast-tracked tested vaccines for prevention. These vaccines have their own adverse effects, which have severely affected the global healthcare system. The discovery of the main protease structure of coronavirus (Mpro/Clpro) has resulted in the identification of compounds having antiviral potential, especially from the herbal system. In this study, the computer-associated drug design tools were utilised to analyze the reported phytoconstituents of Nigella sativa for their antiviral activity against the main protease. Fifty-eight compounds were subjected to pharmacological parameter analysis to determine their lead likeness in comparison to the standard drugs (chloroquine and nirmatrelvir) used in the treatment of SARS-CoV-2. Nearly 31 compounds were docked against five different SARS-CoV-2 main proteases, and all compounds showed better binding affinity and inhibition constant against the proteases. However, dithymoquinone and campesterol displayed the best binding scores and hence were further subjected to dynamics and MMPBSA study for 100 ns. The stability analysis shows that dithymoquinone and campesterol show less variation in fluctuation in residues compared to standard complexes. Moreover, dithymoquinone exhibited higher binding affinity and favorable interaction followed by campesterol as compared to the standard drug. The in silico computational analysis provides a promising hit for regulating the main proteases activity.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Abdullah Algaissi
- Department of Medical Laboratories Technology, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia
- Emerging and Epidemic Infectious Diseases Research Unit, Medical Research Center, Jazan University, Jazan, Saudi Arabia
| | - Elhan Khan
- Natural Products Laboratory, Department of Bioengineering, Integral University, Lucknow, Uttar Pradesh, India
| | - Heena Tabassum
- Dr. D. Y. Patil Biotechnology and Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth, Pune, Maharashtra, India
| | - Sadiyah Samreen
- Natural Products Laboratory, Department of Bioengineering, Integral University, Lucknow, Uttar Pradesh, India
| | - Nizar A Khamjan
- Department of Medical Laboratories Technology, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia
| | - Mohtashim Lohani
- Medical Research Centre, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia
| | - Saif Khan
- Department of Basic Dental and Medical Sciences, College of Dentistry, Ha'il University, Ha'il, Saudi Arabia
| | - Nader Kameli
- Department of Medical Laboratories Technology, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia
| | - Faisal Madkhali
- Department of Medical Laboratories Technology, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia
| | - Iffat Zareen Ahmad
- Natural Products Laboratory, Department of Bioengineering, Integral University, Lucknow, Uttar Pradesh, India
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Yuan D, Du J, Xin M, Bai G, Zhang C, Liu G. Influence of myoglobin on the antibacterial activity of carvacrol and the binding mechanism between the two compounds. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2024; 104:1063-1073. [PMID: 37743570 DOI: 10.1002/jsfa.13005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/30/2023] [Accepted: 09/25/2023] [Indexed: 09/26/2023]
Abstract
BACKGROUND Myoglobin (MB), a pigmentation protein, can adversely affect the antibacterial activity of carvacrol (CAR) and weaken its bacteriostasis effect. This study aimed to clarify the influence of MB on the antibacterial activity of CAR and ascertain the mechanism involved in the observed influence, especially the interaction between the two compounds. RESULTS Microbiological analysis indicated that the presence of MB significantly suppressed the antibacterial activity of CAR against Listeria monocytogenes. Ultraviolet-visible spectrometry and fluorescence spectroscopic analysis confirmed the interaction between CAR and MB. The stoichiometric number was determined as ~0.7 via double logarithmic Stern-Volmer equation analysis, while thermodynamic analysis showed that the conjugation of the two compounds occurred as an exothermal reaction (ΔH° = -32.3 ± 11.4 kJ mol-1 and ΔS° = -75 J mol-1 K-1 ). Circular dichroism, Fourier transform infrared spectroscopy and nuclear magnetic resonance spectroscopy showed hydrogen bonding in the carvacrol-myoglobin complex (CAR-MB). Molecular docking analysis confirmed that amino acid residues, including GLY80 and HIS82, were most likely to form hydrogen bonds with CAR, while hydrogen bonds represented the main driving force for CAR-MB formation. CONCLUSION CAR antibacterial activity was significantly inhibited by the presence of MB in the environment due to the notable reduction in the effective concentration of CAR caused by CAR-MB formation. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Dongdong Yuan
- Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Ministry of Education, School of Food and Health, Beijing Technology and Business University, Beijing, China
- Beijing Engineering and Technology Research Center of Food Additives, School of Food and Health, Beijing Technology and Business University, Beijing, China
| | - Jing Du
- Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Ministry of Education, School of Food and Health, Beijing Technology and Business University, Beijing, China
- Beijing Engineering and Technology Research Center of Food Additives, School of Food and Health, Beijing Technology and Business University, Beijing, China
| | - Mengna Xin
- Beijing Engineering and Technology Research Center of Food Additives, School of Food and Health, Beijing Technology and Business University, Beijing, China
- China Food Flavor and Nutrition Health Innovation Center, School of Food and Health, Beijing Technology and Business University, Beijing, China
| | - Guohui Bai
- Beijing Engineering and Technology Research Center of Food Additives, School of Food and Health, Beijing Technology and Business University, Beijing, China
- China Food Flavor and Nutrition Health Innovation Center, School of Food and Health, Beijing Technology and Business University, Beijing, China
| | - Chan Zhang
- Beijing Engineering and Technology Research Center of Food Additives, School of Food and Health, Beijing Technology and Business University, Beijing, China
- China Food Flavor and Nutrition Health Innovation Center, School of Food and Health, Beijing Technology and Business University, Beijing, China
| | - Guorong Liu
- Key Laboratory of Geriatric Nutrition and Health (Beijing Technology and Business University), Ministry of Education, School of Food and Health, Beijing Technology and Business University, Beijing, China
- Beijing Engineering and Technology Research Center of Food Additives, School of Food and Health, Beijing Technology and Business University, Beijing, China
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Fan W, Liu J, Liu Q. Exploring the potential mechanism and molecular targets of Taohong Siwu Decoction against deep vein thrombosis based on network pharmacology and analysis docking. Medicine (Baltimore) 2024; 103:e36220. [PMID: 38215128 PMCID: PMC10783296 DOI: 10.1097/md.0000000000036220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 10/30/2023] [Indexed: 01/14/2024] Open
Abstract
This study aims to investigate the mechanism of Taohong Siwu Decoction (THSWD) against deep vein thrombosis (DVT) using network pharmacology and molecular docking technology. We used the Traditional Chinese Medicine Systems Pharmacology database and reviewed literature to identify the main chemical components of THSWD. To find targets for DVT, we consulted GeneCards, Therapeutic Target Database, and PharmGKB databases. We used Cytoscape 3.8.2 software to construct herb-disease-gene-target networks. Additionally, we integrated drug targets and disease targets on the STRING platform to create a protein-protein interaction network. Then, we conducted Kyoto Encyclopedia of Genes and Genomes and gene ontology analysis. Finally, We employed the molecular docking method to validate our findings. We identified 56 potential targets associated with DVT and found 61 effective components. beta-sitosterol, quercetin, and kaempferol were the most prominent among these components. Our analysis of the protein-protein interaction network revealed that IL6, L1B, and AKT1 had the highest degree of association. Gene ontology analysis showed that THSWD treatment for DVT may involve response to inorganic substances, negative regulation of cell differentiation, plasma membrane protein complex, positive regulation of phosphorylation, and signaling receptor regulator activity. Kyoto Encyclopedia of Genes and Genomes analysis indicated that lipid and atherosclerosis, pathways in cancer, as well as the PI3K-Akt pathway are the main signal pathways involved. Molecular docking results demonstrated strong binding affinity between beta-sitosterol, quercetin, kaempferol, and AKT1 proteins as well as IL1B and IL6 proteins. The main targets for THSWD treatment of DVT may include AKT1, IL1B, and IL6. Beta-sitosterol, quercetin, and kaempferol may be the active ingredients responsible for producing this effect. These compounds may slow down the progression of DVT by regulating the inflammatory response through the PI3K/Akt pathway.
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Affiliation(s)
- Wei Fan
- Department of Orthopaedics, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
- Sichuan Provincial Laboratory of Orthopaedic Engineering, Luzhou, Sichuan, China
| | - Jinhui Liu
- Department of Orthopaedics, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
- Sichuan Provincial Laboratory of Orthopaedic Engineering, Luzhou, Sichuan, China
| | - Qingyan Liu
- The Operating Room, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
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Khan MU, Basist P, Gaurav, Zahiruddin S, Penumallu NR, Ahmad S. Ameliorative effect of traditional polyherbal formulation on TNF-α, IL-1β and Caspase-3 expression in kidneys of wistar rats against sodium fluoride induced oxidative stress. JOURNAL OF ETHNOPHARMACOLOGY 2024; 318:116900. [PMID: 37442489 DOI: 10.1016/j.jep.2023.116900] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 07/05/2023] [Accepted: 07/08/2023] [Indexed: 07/15/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Sharbat-e-bazoori Motadil (SBM) is a polyherbal formulation that have been used for centuries as a part of the Unani system of medicine for renal disease. AIM OF THE STUDY The objective of this study was to explore and validate the nephroprotective potential of sugar-free SBM (SF-SBM) and its mechanisms of action against sodium fluoride (NaF)-induced nephrotoxicity in HEK-293 cells. Additionally, the study aimed to assess the quality control of SF-SBM and investigate its effects using an in vivo rat model with pattern recognition following oral administration of SF-SBM. MATERIALS AND METHODS The nephroprotective effect of SF-SBM was investigated using both an HEK-293 cell line and Wistar rats. Nephrotoxicity was induced in these models by administering NaF at a concentration of 600 ppm (parts per million) for a duration of seven days. The SF-SBM formulation was standardized using high-performance thin-layer chromatography (HPTLC) to assess the presence of marker compounds, namely gallic acid, quercetin, and ferulic acid. Metabolite characterization of SF-SBM was carried out using ultra-high-performance liquid chromatography mass spectrometry (UPLC-MS) with a monolithic capillary silica-based C18 column. This analytical technique allowed for the identification of bioactive substances and verification of the identified markers. Acute toxicity of SF-SBM was evaluated in Wistar rats by administering a single oral dose of 2000 mg/kg of SF-SBM. The nephroprotective efficacy of SF-SBM was further assessed at low (LD), medium (MD) and high (HD) doses of 32.1, 64.2, and 128.4 mg/kg, respectively, administered orally. Nephrotoxicity was induced in Wistar rats by adding NaF to their drinking water for seven days. Biochemical and urine markers were analyzed to evaluate the antioxidant, inflammatory, and apoptotic potential of SF-SBM. Additionally, histopathological analysis and immunohistochemical alterations in the expression of caspase-3 and nicotinamide adenine dinucleotide phosphate (NADPH) oxidase-4 (NOX-4) in kidney tissue were performed to confirm the findings of the in vivo experiments. Furthermore, in vivo pattern recognition of SF-SBM metabolites, identified through GC-MS metabolomics, and in-silico docking analysis of major metabolites in plasma were conducted to gain further insights. RESULT Phytochemical analysis using HPTLC, TLC-bioautography, and UPLC-MS revealed the presence of several bioactive constituents in SF-SBM, including ferulic acid, gallic acid (GA), ellagic acid, quercetin, and apigenin. These compounds exhibit diverse pharmacological properties. In vitro studies demonstrated the protective effect of SF-SBM on HEK-293 cell line against nephrotoxicity. The acute toxicity study of SF-SBM at a dose of 2000 mg/kg showed no mortality or signs of toxicity throughout the 14-day observation period. In the in vivo studies, administration of NaF resulted in significant elevation (P < 0.001) of biochemical and urine parameters, indicating oxidative, inflammatory, and apoptotic stress. Histopathological examination revealed severe depletion of Bowman's capsule, and immunohistochemistry demonstrated negative immunostaining for caspase-3 and reduced NOX-4 reactions. Pre-treatment with SF-SBM significantly attenuated the elevated biochemical and urine markers, restored the antioxidant enzyme levels (such as SOD, CAT, GSH, GPx and NO), and regulated the expression of inflammatory cytokines (TNF-α, IL-1β, CASP-3) in kidney tissue at doses of SF-SBM-MD (64.2 mg/kg) and SF-SBM-HD (128.4 mg/kg), showing comparable results to those of α-Ketoanalogue. Histopathological assessment demonstrated improvements in tissue damage. Pattern recognition analysis of SF-SBM identified the presence of 56 metabolites at different time intervals. Additionally, in-silico studies revealed strong interactions of SF-SBM with a binding energy of -6.5 and -5.6 kcal for 4C2N. CONCLUSION The phytoconstituents present in SF-SBM play a crucial role in its nephroprotective action by acting as potent antioxidants and reducing proinflammatory and apoptotic damage in rat cells. This indicates that SF-SBM has promising potential for the treatment of nephrotoxicity.
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Affiliation(s)
- Mohammad Umar Khan
- Centre of Excellence in Unani Medicine (Pharmacognosy & Pharmacology), Jamia Hamdard, New Delhi, 110062, India; Bioactive Natural Product Laboratory, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, 110062, India; Department of Food Technology, School of Interdisciplinary Science and Technology, Jamia Hamdard, New Delhi, 110062, India
| | - Parakh Basist
- Centre of Excellence in Unani Medicine (Pharmacognosy & Pharmacology), Jamia Hamdard, New Delhi, 110062, India; Bioactive Natural Product Laboratory, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, 110062, India
| | - Gaurav
- Centre of Excellence in Unani Medicine (Pharmacognosy & Pharmacology), Jamia Hamdard, New Delhi, 110062, India; Bioactive Natural Product Laboratory, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, 110062, India; IIMT College of Medical Sciences, IIMT University, O Pocket Ganga Nagar Meerut, Uttar Pradesh, 250001, India
| | - Sultan Zahiruddin
- Centre of Excellence in Unani Medicine (Pharmacognosy & Pharmacology), Jamia Hamdard, New Delhi, 110062, India; Bioactive Natural Product Laboratory, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, 110062, India
| | - Naveen Reddy Penumallu
- Centre of Excellence in Unani Medicine (Pharmacognosy & Pharmacology), Jamia Hamdard, New Delhi, 110062, India; Bioactive Natural Product Laboratory, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, 110062, India
| | - Sayeed Ahmad
- Centre of Excellence in Unani Medicine (Pharmacognosy & Pharmacology), Jamia Hamdard, New Delhi, 110062, India; Bioactive Natural Product Laboratory, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi, 110062, India; Department of Food Technology, School of Interdisciplinary Science and Technology, Jamia Hamdard, New Delhi, 110062, India.
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Sarma S, Dowerah D, Basumatary M, Phonglo A, Deka RC. Inhibitory potential of furanocoumarins against cyclin dependent kinase 4 using integrated docking, molecular dynamics and ONIOM methods. J Biomol Struct Dyn 2024:1-30. [PMID: 38189343 DOI: 10.1080/07391102.2023.2300755] [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: 10/04/2023] [Accepted: 12/23/2023] [Indexed: 01/09/2024]
Abstract
Cyclin Dependent Kinase 4 (CDK4) is vital in the process of cell-cycle and serves as a G1 phase checkpoint in cell division. Selective antagonists of CDK4 which are in use as clinical chemotherapeutics cause various side-effects in patients. Furanocoumarins induce anti-cancerous effects in a range of human tumours. Therefore, targeting these compounds against CDK4 is anticipated to enhance therapeutic effectiveness. This work intended to explore the CDK4 inhibitory potential of 50 furanocoumarin molecules, using a comprehensive approach that integrates the processes of docking, drug-likeness, pharmacokinetic analysis, molecular dynamics simulations and ONIOM (Our own N-layered Integrated molecular Orbital and Molecular mechanics) methods. The top five best docked compounds obtained from docking studies were screened for subsequent analysis. The molecules displayed good pharmacokinetic properties and no toxicity. Epoxybergamottin, dihydroxybergamottin and notopterol were found to inhabit the ATP-binding zone of CDK4 with substantial stability and negative binding free energy forming hydrogen bonds with key catalytic residues of the protein. Notopterol exhibiting the highest binding energy was subjected to ONIOM calculations wherein the hydrogen bonding interactions were retained with significant negative interaction energy. Hence, through these series of computerised methods, notopterol was screened as a potent CDK4 inhibitor and can act as a starting point in successive processes of drug design.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Srutishree Sarma
- CMML-Catalysis and Molecular Modelling Lab, Department of Chemical Sciences, Tezpur University, Sonitpur, Assam, India
| | - Dikshita Dowerah
- CMML-Catalysis and Molecular Modelling Lab, Department of Chemical Sciences, Tezpur University, Sonitpur, Assam, India
| | - Moumita Basumatary
- CMML-Catalysis and Molecular Modelling Lab, Department of Chemical Sciences, Tezpur University, Sonitpur, Assam, India
| | - Ambalika Phonglo
- CMML-Catalysis and Molecular Modelling Lab, Department of Chemical Sciences, Tezpur University, Sonitpur, Assam, India
| | - Ramesh Ch Deka
- CMML-Catalysis and Molecular Modelling Lab, Department of Chemical Sciences, Tezpur University, Sonitpur, Assam, India
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Chhabra S, Mehan S, Khan Z, Gupta GD, Narula AS. Matrine mediated neuroprotective potential in experimental multiple sclerosis: Evidence from CSF, blood markers, brain samples and in-silico investigations. J Neuroimmunol 2023; 384:578200. [PMID: 37774554 DOI: 10.1016/j.jneuroim.2023.578200] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 09/12/2023] [Indexed: 10/01/2023]
Abstract
Multiple sclerosis (MS) is a debilitating, inflammatory, and demyelinating disease of the central nervous system influenced by environmental and genetic factors. Around 2.8 million people worldwide are affected by MS due to its challenging diagnosis and treatment. Our study investigates the role of the JAK/STAT and PPAR-gamma signaling pathways in the progression of multiple sclerosis. Inflammation and demyelination can be caused by dysregulation of these pathways. Modulating the STAT-3, mTOR, and PPAR-gamma signaling pathways may offer therapeutic potential for multiple sclerosis. Matrine (40 and 80 mg/kg, i.p.), a quinolizidine alkaloid derived from Sophora flavescens, has been investigated for its therapeutic potential in our laboratory. Matrine has been studied for its neuroprotective effect in neurodegenerative diseases. It inhibits inflammatory responses and promotes regeneration of damaged myelin sheaths, indicating its potential efficacy in treating multiple sclerosis. Matrine exerts its neuroprotective effect by inhibiting STAT-3 and mTOR and promoting PPAR-gamma expression.GW9662, a PPAR-gamma antagonist (2 mg/kg, i.p.), was administered to evaluate the involvement of PPAR-gamma and to compare the efficacy of matrine's potential neuroprotective effect. Matrine's interaction with the STAT-3, mTOR, and PPAR-gamma pathways in multiple Sclerosis was also validated and confirmed through insilico investigation. In addition, matrine altered the CBC profile, intensifying the clinical presentation of multiple sclerosis. In addition, we evaluated the diagnostic potential of various biological samples, including CSF, blood plasma, and brain homogenates (striatum, cortex, hippocampus, and midbrain). These samples were used to evaluate the neurochemical changes caused by neurobehavioral alterations during the progression of multiple sclerosis. These results indicate that matrine treatment ameliorated multiple sclerosis and that the mechanism underlying these effects may be closely related to the modulation of the STAT-3/mTOR/PPAR-gamma signaling pathway.
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Affiliation(s)
- Swesha Chhabra
- Division of Neuroscience, Department of Pharmacology, ISF College of Pharmacy, Moga, Punjab, India
| | - Sidharth Mehan
- Division of Neuroscience, Department of Pharmacology, ISF College of Pharmacy, Moga, Punjab, India.
| | - Zuber Khan
- Division of Neuroscience, Department of Pharmacology, ISF College of Pharmacy, Moga, Punjab, India
| | | | - Acharan S Narula
- Narula Research, LLC, 107 Boulder Bluff, Chapel Hill, NC 27516, USA
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Sumon MAA, Asseri AH, Molla MHR, Aljahdali MO, Hasan MR, Rahman MA, Hasan MT, Sumon TA, Gabr MH, Islam MS, Fakhurji B, Moulay M, Larson E, Brown CL. Identification of natural antiviral drug candidates against Tilapia Lake Virus: Computational drug design approaches. PLoS One 2023; 18:e0287944. [PMID: 37939069 PMCID: PMC10631680 DOI: 10.1371/journal.pone.0287944] [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: 06/16/2023] [Accepted: 10/13/2023] [Indexed: 11/10/2023] Open
Abstract
Tilapia Lake Virus (TiLV) is a disease that affects tilapia fish, causing a high rate of sudden death at any stage in their life cycle. Unfortunately, there are currently no effective antiviral drugs or vaccines to prevent or control the progression of this disease. Researchers have discovered that the CRM1 protein plays a critical function in the development and spreading of animal viruses. By inhibiting CRM1, the virus's spread in commercial fish farms can be suppressed. With this in mind, this study intended to identify potential antiviral drugs from two different tropical mangrove plants from tropical regions: Heritiera fomes and Ceriops candolleana. To identify promising compounds that target the CRM1 protein, a computer-aided drug discovery approach is employed containing molecular docking, ADME (absorption, distribution, metabolism and excretion) analysis, toxicity assessment as well as molecular dynamics (MD) simulation. To estimate binding affinities of all phytochemicals, molecular docking is used and the top three candidate compounds with the highest docking scores were selected, which are CID107876 (-8.3 Kcal/mol), CID12795736 (-8.2 Kcal/mol), and CID12303662 (-7.9 Kcal/mol). We also evaluated the ADME and toxicity properties of these compounds. Finally, MD simulation was conducted to analyze the stability of the protein-ligand complex structures and confirm the suitability of these compounds. The computational study demonstrated that the phytochemicals found in H. fomes and C. candolleana could potentially serve as important inhibitors of TiLV, offering practical utility. However, further in vivo investigations are necessary to investigate and potentially confirm the effectiveness of these compounds as antiviral drugs against the virus TiLV.
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Affiliation(s)
- Md Afsar Ahmed Sumon
- Department of Marine Biology, Faculty of Marine Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Amer H. Asseri
- Department of Biochemistry, Faculty of Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | | | - Md. Rifat Hasan
- Department of Applied Mathematics, Faculty of Science, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - M. Aminur Rahman
- Department of Fisheries and Marine Bioscience, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Md. Tawheed Hasan
- Department of Aquaculture, Sylhet Agricultural University, Sylhet, Bangladesh
| | - Tofael Ahmed Sumon
- Department of Fish Health Management, Sylhet Agricultural University, Sylhet, Bangladesh
| | - Mohamed Hosny Gabr
- Department of Marine Biology, Faculty of Marine Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Md. Shafiqul Islam
- Institute of Marine Sciences, University of Chittagong, Chittagong, Bangladesh
| | - Burhan Fakhurji
- iGene Medical Training and Molecular Research Center, Jeddah, Saudi Arabia
| | - Mohammed Moulay
- Embryonic Stem Cell Research Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Earl Larson
- Department of Microbiology, St Johns River State College, Orange Park, FL, United States of America
| | - Christopher L. Brown
- FAO World Fisheries University Pilot Programme, Pukyong National University, Busan, South Korea
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Giri A, Mehan S, Khan Z, Gupta GD, Narula AS. Melatonin-mediated IGF-1/GLP-1 activation in experimental OCD rats: Evidence from CSF, blood plasma, brain and in-silico investigations. Biochem Pharmacol 2023; 217:115831. [PMID: 37777162 DOI: 10.1016/j.bcp.2023.115831] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 09/14/2023] [Accepted: 09/25/2023] [Indexed: 10/02/2023]
Abstract
Obsessive-compulsive disorder (OCD) is a neuropsychiatric condition characterized by intrusive, repetitive thoughts and behaviors. Our study uses a validated 8-OH-DPAT-induced experimental model of OCD in rodents. We focus on the modulatory effects of Insulin-like growth factor-1 (IGF-1) and glucagon-like peptide-1 (GLP-1), which are linked to neurodevelopment and survival. Current research investigates melatonin, a molecule with neuroprotective properties and multiple functions. Melatonin has beneficial effects on various illnesses, including Alzheimer's, Parkinson's, and depression, indicating its potential efficacy in treating OCD. In the present study, we employed two doses of melatonin, 5 mg/kg and 10 mg/kg, demonstrating a dose-dependent effect on 8-OH-DPAT-induced rat changes. In addition, the melatonin antagonist luzindole 5 mg/kg was utilized to compare and validate the efficacy of melatonin. In-silico studies alsocontribute to understanding the activation of IGF-1/GLP-1 pathways by melatonin. Current research indicates restoring neurochemical measurements on various biological samples (brain homogenates, CSF, and blood plasma) and morphological and histological analyses. In addition, the current research seeks to increase understanding of OCD and investigate potential new treatment strategies. Therefore, it is evident from the aforementioned research that the protective effect of melatonin can serve as a strong basis for developing a new OCD treatment by upregulating IGF-1 and GLP-1 levels. The primary focus of current study revolves around the examination of melatonin as an activator of IGF-1/GLP-1, with the aim of potentially mitigating behavioral, neurochemical, and histopathological abnormalities in an experimental model of obsessive-compulsive disorder caused by 8-OH-DPAT in adult Wistar rats.
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Affiliation(s)
- Aditi Giri
- Division of Neuroscience, Department of Pharmacology, ISF College of Pharmacy, (Affiliated to IK Gujral Punjab Technical University, Jalandhar, Punjab, 144603, India), Moga, Punjab, India
| | - Sidharth Mehan
- Division of Neuroscience, Department of Pharmacology, ISF College of Pharmacy, (Affiliated to IK Gujral Punjab Technical University, Jalandhar, Punjab, 144603, India), Moga, Punjab, India.
| | - Zuber Khan
- Division of Neuroscience, Department of Pharmacology, ISF College of Pharmacy, (Affiliated to IK Gujral Punjab Technical University, Jalandhar, Punjab, 144603, India), Moga, Punjab, India
| | - Ghanshyam Das Gupta
- Department of Pharmaceutics, ISF College of Pharmacy, (Affiliated to IK Gujral Punjab Technical University, Jalandhar, Punjab, 144603, India), Moga, Punjab, India
| | - Acharan S Narula
- Narula Research, LLC, 107 Boulder Bluff, Chapel Hill, NC 27516, USA
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Ballinas-Indilí R, Nicolás-Vázquez MI, Martínez J, Ramírez-Apan MT, Álvarez-Toledano C, Toscano A, Hernández-Rodríguez M, Mera Jiménez E, Miranda Ruvalcaba R. Synthesis, Cytotoxic Activity and In Silico Study of Novel Dihydropyridine Carboxylic Acids Derivatives. Int J Mol Sci 2023; 24:15414. [PMID: 37895094 PMCID: PMC10607468 DOI: 10.3390/ijms242015414] [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: 09/08/2023] [Revised: 10/11/2023] [Accepted: 10/18/2023] [Indexed: 10/29/2023] Open
Abstract
To aid the possible prevention of multidrug resistance in tumors and cause lower toxicity, a set of sixteen novel dihydropyridine carboxylic acids derivatives 3a-p were produced; thus, the activation of various ynones with triflic anhydride was performed, involving a nucleophilic addition of several bis(trimethylsilyl) ketene acetals, achieving good yields requiring easy workup. The target molecules were unequivocally characterized by common spectroscopic methods. In addition, two of the tested compounds (3a, and 3b) were selected to perform in silico studies due to the highest cytotoxic activity towards the HCT-15 cell line (7.94 ± 1.6 μM and 9.24 ± 0.9 μM, respectively). Employing theoretical calculations with density functional theory (DFT) using the B3LYP/6-311++G(d,p) showed that the molecular parameters correlate adequately with the experimental results. In contrast, predictions employing Osiris Property Explorer showed that compounds 3a and 3b present physicochemical characteristics that would likely make it an orally active drug. Moreover, the performance of Docking studies with proteins related to the apoptosis pathway allowed a proposal of which compounds could interact with PARP-1 protein. Pondering the obtained results (synthesis, in silico, and cytotoxic activity) of the target compounds, they can be judged as suitable antineoplastic agent candidates.
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Affiliation(s)
- Ricardo Ballinas-Indilí
- Departamento de Ciencias Químicas, Facultad de Estudios Superiores Cuautitlán Campo 1, Universidad Nacional Autónoma de México, Avenida 1o de Mayo s/n, Colonia Santa María las Torres, Cuautitlán Izcalli 54740, Mexico; (R.B.-I.); (M.I.N.-V.); (J.M.)
| | - María Inés Nicolás-Vázquez
- Departamento de Ciencias Químicas, Facultad de Estudios Superiores Cuautitlán Campo 1, Universidad Nacional Autónoma de México, Avenida 1o de Mayo s/n, Colonia Santa María las Torres, Cuautitlán Izcalli 54740, Mexico; (R.B.-I.); (M.I.N.-V.); (J.M.)
| | - Joel Martínez
- Departamento de Ciencias Químicas, Facultad de Estudios Superiores Cuautitlán Campo 1, Universidad Nacional Autónoma de México, Avenida 1o de Mayo s/n, Colonia Santa María las Torres, Cuautitlán Izcalli 54740, Mexico; (R.B.-I.); (M.I.N.-V.); (J.M.)
| | - María Teresa Ramírez-Apan
- Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Mexico City 04510, Mexico; (M.T.R.-A.); (C.Á.-T.); (A.T.)
| | - Cecilio Álvarez-Toledano
- Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Mexico City 04510, Mexico; (M.T.R.-A.); (C.Á.-T.); (A.T.)
| | - Alfredo Toscano
- Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, Mexico City 04510, Mexico; (M.T.R.-A.); (C.Á.-T.); (A.T.)
| | - Maricarmen Hernández-Rodríguez
- Laboratorio de Cultivo Celular, Sección de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico City 11340, Mexico; (M.H.-R.); (E.M.J.)
| | - Elvia Mera Jiménez
- Laboratorio de Cultivo Celular, Sección de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico City 11340, Mexico; (M.H.-R.); (E.M.J.)
| | - René Miranda Ruvalcaba
- Departamento de Ciencias Químicas, Facultad de Estudios Superiores Cuautitlán Campo 1, Universidad Nacional Autónoma de México, Avenida 1o de Mayo s/n, Colonia Santa María las Torres, Cuautitlán Izcalli 54740, Mexico; (R.B.-I.); (M.I.N.-V.); (J.M.)
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Majrashi TA, Wahab S, Almoyad MAA, Alkhathami AG, Alshahrani MY. Exploring natural compound, Panicutine as leucine-rich repeat kinase 2 inhibitor against Parkinson's disease: a structure-guided approach. J Biomol Struct Dyn 2023:1-10. [PMID: 37837424 DOI: 10.1080/07391102.2023.2268183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 09/29/2023] [Indexed: 10/16/2023]
Abstract
Leucine-rich repeat kinase 2 (LRRK2) is a promising drug target for the therapeutic management of Parkinson's disease (PD) and other neurodegenerative disorders. LRRK2 inhibitors have the potential to modulate neuroinflammation, reduce alpha-synuclein aggregation and improve motor symptoms in PD patients. Although LRRK2 inhibitors are still in the early stages of clinical development, the identification of potent and selective inhibitors through structure-guided approaches provides a promising avenue for the development of effective therapies for PD and other neurodegenerative disorders. In this study, natural compounds from the IMPPAT database were screened using a state-of-the-art computational virtual screening approach to identify potential inhibitors of LRRK2. We carried out a docking screening on a library of natural compounds and identified a few compounds with strong binding affinity, docking score and specificity towards LRRK2 as the top hits. These hits were then subjected to further analysis based on multiple parameters for the Pan-assay interference compounds and their physicochemical and pharmacokinetics evaluation followed by a detailed interaction analysis. After careful evaluation, one natural compound, Panicutine, was identified as a promising candidate for LRRK2 due to its significant affinity and specificity towards the LRRK2 binding pocket. Additionally, it exhibited drug-like properties with blood-brain barrier permeability as determined by ADMET properties. To gain a deeper understanding of the stability and conformational changes of the LRRK2-ligand complex, MD simulations were conducted for 100 nanoseconds under explicit solvent conditions followed by principal component analysis and free energy dynamics. The simulation results demonstrated that the LRRK2-Panicutine complex remained stable throughout the simulation trajectories. Based on these findings, it is concluded that Panicutine has the potential to act as a LRRK2 inhibitor against PD and other neurodegenerative disorders.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Taghreed A Majrashi
- Department of Pharmacognosy, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
| | - Shadma Wahab
- Department of Pharmacognosy, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
| | - Mohammad Ali Abdullah Almoyad
- Department of Basic Medical Sciences, College of Applied Medical Sciences in Khamis Mushyt, King Khalid University, Abha, Saudi Arabia
| | - Ali Gaithan Alkhathami
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
| | - Mohammad Y Alshahrani
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
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Muralitharan D, Varadharajan V, Venkidasamy B. Cheminformatics and systems pharmacology approaches to unveil the potential plant bioactives to combat COVID-19. J Mol Recognit 2023; 36:e3055. [PMID: 37658788 DOI: 10.1002/jmr.3055] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 08/17/2023] [Accepted: 08/18/2023] [Indexed: 09/05/2023]
Abstract
COVID-19 was a global pandemic in the year 2020. Several treatment options failed to cure the disease. Thus, plant-based medicines are becoming a trend nowadays due to their less side effects. Bioactive chemicals from natural sources have been utilised for centuries as treatment options for a variety of ailments. To find out the potent bioactive compounds to counteract COVID-19, we use systems pharmacology and cheminformatics. They use the definitive data and predict the possible outcomes. In this study, we collected a total of 72 phytocompounds from the medicinally important plants such as Garcinia mangostana and Cinnamomum verum, of which 13 potential phytocompounds were identified to be active against the COVID-19 infection based on Swiss Target Prediction and compound target network analysis. These phytocompounds were annotated to identify the specific human receptor that targets COVID-19-specific genes such as MAPK8, MAPK14, ACE, CYP3A4, TLR4 and TYK2. Among these, compounds such as smeathxanthone A, demethylcalabaxanthone, mangostanol, trapezifolixanthone from Garcinia mangostana and camphene from C. verum were putatively target various COVID-19-related genes. Molecular docking results showed that smeathxanthone A and demethylcalabaxanthone exhibit increased binding efficiency towards the COVID-19-related receptor proteins. These compounds also showed efficient putative pharmacoactive properties than the commercial drugs ((R)-remdesivir, favipiravir and hydroxychloroquine) used to cure COVID-19. In conclusion, our study highlights the use of cheminformatics approach to unravel the potent and novel phytocompounds against COVID-19. These phytocompounds may be safer to use, more efficient and less harmful. This study highlights the value of natural products in the search for new drugs and identifies candidates with great promise.
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Affiliation(s)
- Dhivyadharshini Muralitharan
- Saveetha Medical College and Hospital, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai, India
| | | | - Baskar Venkidasamy
- Department of Oral & Maxillofacial Surgery, Saveetha Dental College and Hospital, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai, India
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Fang K, Zhang Y, Du S, He J. ColdDTA: Utilizing data augmentation and attention-based feature fusion for drug-target binding affinity prediction. Comput Biol Med 2023; 164:107372. [PMID: 37597410 DOI: 10.1016/j.compbiomed.2023.107372] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 07/26/2023] [Accepted: 08/12/2023] [Indexed: 08/21/2023]
Abstract
Accurate prediction of drug-target affinity (DTA) plays a crucial role in drug discovery and development. Recently, deep learning methods have shown excellent predictive performance on randomly split public datasets. However, verifications are still required on this splitting method to reflect real-world problems in practical applications. And in a cold-start experimental setup, where drugs or proteins in the test set do not appear in the training set, the performance of deep learning models often significantly decreases. This indicates that improving the generalization ability of the models remains a challenge. To this end, in this study, we propose ColdDTA: using data augmentation and attention-based feature fusion to improve the generalization ability of predicting drug-target binding affinity. Specifically, ColdDTA generates new drug-target pairs by removing subgraphs of drugs. The attention-based feature fusion module is also used to better capture the drug-target interactions. We conduct cold-start experiments on three benchmark datasets, and the consistency index (CI) and mean square error (MSE) results on the Davis and KIBA datasets show that ColdDTA outperforms the five state-of-the-art baseline methods. Meanwhile, the results of area under the receiver operating characteristic (ROC-AUC) on the BindingDB dataset show that ColdDTA also has better performance on the classification task. Furthermore, visualizing the model weights allows for interpretable insights. Overall, ColdDTA can better solve the realistic DTA prediction problem. The code has been available to the public.
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Affiliation(s)
- Kejie Fang
- Faculty of Electrical Engineering and Computer Science, Ningbo University, Ningbo, 315211, China
| | - Yiming Zhang
- Engineering Laboratory of Advanced Energy Materials, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo, 315201, China
| | - Shiyu Du
- Engineering Laboratory of Advanced Energy Materials, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo, 315201, China; School of Materials Science and Engineering and School of Computer Science, China University of Petroleum (East China), Qingdao, 266580, China.
| | - Jian He
- State Key Laboratory of Systems Medicine for Cancer, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
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Kumar S, Ali I, Abbas F, Rana A, Pandey S, Garg M, Kumar D. In-silico design, pharmacophore-based screening, and molecular docking studies reveal that benzimidazole-1,2,3-triazole hybrids as novel EGFR inhibitors targeting lung cancer. J Biomol Struct Dyn 2023:1-23. [PMID: 37646177 DOI: 10.1080/07391102.2023.2252496] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 08/18/2023] [Indexed: 09/01/2023]
Abstract
Lung cancer is a complex and heterogeneous disease, which has been associated with various molecular alterations, including the overexpression and mutations of the epidermal growth factor receptor (EGFR). In this study, designed a library of 1843 benzimidazole-1,2,3-triazole hybrids and carried out pharmacophore-based screening to identify potential EGFR inhibitors. The 164 compounds were further evaluated using molecular docking and molecular dynamics simulations to understand the binding interactions between the compounds and the receptor. In-si-lico ADME and toxicity studies were also conducted to assess the drug-likeness and safety of the identified compounds. The results of this study indicate that benzimidazole-1,2,3-triazole hybrids BENZI-0660, BENZI-0125, BENZI-0279, BENZI-0415, BENZI-0437, and BENZI-1110 exhibit dock scores of -9.7, -9.6, -9.6, -9.6, -9.6, -9.6 while referencing molecule -7.9 kcal/mol for EGFR (PDB ID: 4HJO), respectively. The molecular docking and molecular dynamics simulations revealed that the identified compounds formed stable interactions with the active site of EGFR, indicating their potential as inhibitors. The in-silico ADME and toxicity studies showed that the compounds had favorable drug-likeness properties and low toxicity, further supporting their potential as therapeutic agents. Finally, performed DFT studies on the best-selected ligands to gain further insights into their electronic properties. The findings of this study provide important insights into the potential of benzimidazole-1,2,3-triazole hybrids as promising EGFR inhibitors for the treatment of lung cancer. This research opens up a new avenue for the discovery and development of potent and selective EGFR inhibitors for the treatment of lung cancer.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sunil Kumar
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Shoolini University, Solan, India
| | - Iqra Ali
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Faheem Abbas
- Key Lab of Organic Optoelectronics and Molecular Engineering of Ministry of Education, Department of Chemistry, Tsinghua University, Beijing, P. R. China
| | - Anurag Rana
- Yogananda School of Artificial Intelligence, Computers, and Data Sciences, Shoolini University, Solan, India
| | - Sadanand Pandey
- Department of Chemistry, College of Natural Science, Yeungnam University, Gyeongsan, Korea
| | - Manoj Garg
- Amity Institute of Molecular Medicine and Stem Cell Research, Amity University, Noida, India
| | - Deepak Kumar
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Shoolini University, Solan, India
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Alsaady IM, Bajrai LH, Alandijany TA, Gattan HS, El-Daly MM, Altwaim SA, Alqawas RT, Dwivedi VD, Azhar EI. Cheminformatics Strategies Unlock Marburg Virus VP35 Inhibitors from Natural Compound Library. Viruses 2023; 15:1739. [PMID: 37632081 PMCID: PMC10459822 DOI: 10.3390/v15081739] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 08/08/2023] [Accepted: 08/12/2023] [Indexed: 08/27/2023] Open
Abstract
The Ebola virus and its close relative, the Marburg virus, both belong to the family Filoviridae and are highly hazardous and contagious viruses. With a mortality rate ranging from 23% to 90%, depending on the specific outbreak, the development of effective antiviral interventions is crucial for reducing fatalities and mitigating the impact of Marburg virus outbreaks. In this investigation, a virtual screening approach was employed to evaluate 2042 natural compounds for their potential interactions with the VP35 protein of the Marburg virus. Average and worst binding energies were calculated for all 20 poses, and compounds that exhibited binding energies <-6 kcal/mol in both criteria were selected for further analysis. Based on binding energies, only six compounds (Estradiol benzoate, INVEGA (paliperidone), Isosilybin, Protopanaxadiol, Permethrin, and Bufalin) were selected for subsequent investigations, focusing on interaction analysis. Among these selected compounds, Estradiol benzoate, INVEGA (paliperidone), and Isosilybin showed strong hydrogen bonds, while the others did not. In this study, the compounds Myricetin, Isosilybin, and Estradiol benzoate were subjected to a molecular dynamics (MD) simulation and free binding energy calculation using MM/GBSA analysis. The reference component Myricetin served as a control. Estradiol benzoate exhibited the most stable and consistent root-mean-square deviation (RMSD) values, whereas Isosilybin showed significant fluctuations in RMSD. The compound Estradiol benzoate exhibited the lowest ΔG binding free energy (-22.89 kcal/mol), surpassing the control compound's binding energy (-9.29 kcal/mol). Overall, this investigation suggested that Estradiol benzoate possesses favorable binding free energies, indicating a potential inhibitory mechanism against the VP35 protein of the Marburg virus. The study proposes that these natural compounds could serve as a therapeutic option for preventing Marburg virus infection. However, experimental validation is required to further corroborate these findings.
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Affiliation(s)
- Isra M. Alsaady
- Special Infectious Agents Unit BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21362, Saudi Arabia; (I.M.A.)
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21362, Saudi Arabia
| | - Leena H. Bajrai
- Special Infectious Agents Unit BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21362, Saudi Arabia; (I.M.A.)
- Biochemistry Department, Faculty of Sciences, King Abdulaziz University, Jeddah 21362, Saudi Arabia
| | - Thamir A. Alandijany
- Special Infectious Agents Unit BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21362, Saudi Arabia; (I.M.A.)
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21362, Saudi Arabia
| | - Hattan S. Gattan
- Special Infectious Agents Unit BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21362, Saudi Arabia; (I.M.A.)
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21362, Saudi Arabia
| | - Mai M. El-Daly
- Special Infectious Agents Unit BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21362, Saudi Arabia; (I.M.A.)
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21362, Saudi Arabia
| | - Sarah A. Altwaim
- Special Infectious Agents Unit BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21362, Saudi Arabia; (I.M.A.)
- Department of Clinical Microbiology and Immunology, Faculty of Medicine, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Rahaf T. Alqawas
- Molecular Diagnostic Laboratory, King Abdulaziz University Hospital, King Abdulaziz University, Jeddah 21362, Saudi Arabia;
| | - Vivek Dhar Dwivedi
- Bioinformatics Research Division, Quanta Calculus, Greater Noida 201310, India
- Center for Global Health Research, Saveetha Institute of Medical and Technical Sciences, Saveetha Medical College and Hospitals, Saveetha University, Tamil Nadu 602105, India
| | - Esam I. Azhar
- Special Infectious Agents Unit BSL3, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21362, Saudi Arabia; (I.M.A.)
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21362, Saudi Arabia
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Kumar S, Ali I, Abbas F, Khan N, Gupta MK, Garg M, Kumar S, Kumar D. In-silico identification of small molecule benzofuran-1,2,3-triazole hybrids as potential inhibitors targeting EGFR in lung cancer via ligand-based pharmacophore modeling and molecular docking studies. In Silico Pharmacol 2023; 11:20. [PMID: 37575679 PMCID: PMC10412522 DOI: 10.1007/s40203-023-00157-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 07/26/2023] [Indexed: 08/15/2023] Open
Abstract
Lung cancer is one of the most common and deadly types of cancer worldwide, and the epidermal growth factor receptor (EGFR) has emerged as a promising therapeutic target for the treatment of this disease. In this study, we designed a library of 1840 benzofuran-1,2,3-triazole hybrids and conducted pharmacophore-based screening to identify potential EGFR inhibitors. The 20 identified compounds were further evaluated using molecular docking and molecular dynamics simulations to understand their binding interactions with the EGFR receptor. In-silico ADME and toxicity studies were also performed to assess their drug-likeness and safety profiles. The results of this study showed the benzofuran-1,2,3-triazole hybrids BENZ-0454, BENZ-0143, BENZ-1292, BENZ-0335, BENZ-0332, and BENZ-1070 dock score of - 10.2, - 10, - 9.9, - 9.8, - 9.7, - 9.6, while reference molecule - 7.9 kcal/mol for EGFR (PDB ID: 4HJO) respectively. The molecular docking and molecular dynamics simulations revealed that the identified compounds formed stable interactions with the active site of the receptor, indicating their potential as inhibitors. The in-silico ADME and toxicity studies suggested that the compounds had good pharmacokinetic and safety profiles, further supporting their potential as therapeutic agents. Finally, performed DFT studies on the best-selected ligands to gain further insights into their electronic properties. The findings of this study provide important insights into the potential of benzofuran-1,2,3-triazole hybrids as promising EGFR inhibitors for the treatment of lung cancer. Overall, this study provides a valuable starting point for the development of novel EGFR inhibitors with improved efficacy and safety profiles. Graphical Abstract Supplementary Information The online version contains supplementary material available at 10.1007/s40203-023-00157-1.
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Affiliation(s)
- Sunil Kumar
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Shoolini University, Solan, Himachal Pradesh 173229 India
| | - Iqra Ali
- Department of Biosciences, COMSATS University Islamabad, Islamabad Campus, Islamabad, 45550 Pakistan
| | - Faheem Abbas
- Key Lab of Organic Optoelectronics and Molecular Engineering of Ministry of Education, Department of Chemistry, Tsinghua University, Beijing, 100084 People’s Republic of China
| | - Nimra Khan
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190 People’s Republic of China
| | - Manoj K. Gupta
- Department of Chemistry, School of Basic Sciences, Central University of Haryana, Mahendergarh, H.R. 123031 India
| | - Manoj Garg
- Amity Institute of Molecular Medicine and Stem Cell Research, Amity University UP, Sector-125, Noida, 201313 India
| | - Saroj Kumar
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Deepak Kumar
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Shoolini University, Solan, Himachal Pradesh 173229 India
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Villada Ramos JA, Aguillón Osma J, Restrepo Cortes B, Loango Chamarro N, Maldonado Celis ME. Identification of potential bioactive compounds of Passiflora edulis leaf extract against colon adenocarcinoma cells. Biochem Biophys Rep 2023; 34:101453. [PMID: 37009402 PMCID: PMC10063390 DOI: 10.1016/j.bbrep.2023.101453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 03/05/2023] [Accepted: 03/06/2023] [Indexed: 03/30/2023] Open
Abstract
Plant bioactive compounds such as flavonoids and triterpenes can affect lipid metabolism. Here, we report the cytotoxic and lipid-lowering activities of the ethanolic extract of P. edulis leaves on human colon adenocarcinoma SW480 cells, also the molecular interactions of bioactive compounds present in P. edulis extract on ACC and HMGCR enzymes. The extract reduced cell viability and decreased intracellular triglyceride content by up to 35% and 28% at 24 and 48 h, respectively; whereas the effect was evident on cholesterol only at 24 h. In-silico analysis revealed that luteolin, chlorogenic acid, moupinamide, isoorientin, glucosyl passionflower, cyclopasifloic acid E and saponarin had optimal molecular coupling on Acetyl-CoA Carboxylase 1 and 2 as well as 3-hydroxy-3-methyl-glutaryl-CoA reductase, with possible inhibitory effects. These results show the ability of ethanolic extract to reduce intracellular levels of cholesterol and triglycerides in SW480 cells, which attracts attention for the treatment of colorectal cancer.
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Fan W, Lan S, Yang Y, Liang J. Network pharmacology prediction and molecular docking-based strategy to discover the potential pharmacological mechanism of Huang-Qi-Gui-Zhi-Wu-Wu decoction against deep vein thrombosis. J Orthop Surg Res 2023; 18:475. [PMID: 37391801 DOI: 10.1186/s13018-023-03948-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 06/22/2023] [Indexed: 07/02/2023] Open
Abstract
BACKGROUND Huangqi Guizhi Wuwu decoction (HQGZWWD) has been used to treat and prevent deep vein thrombosis (DVT) in China. However, its potential mechanisms of action remain unclear. This study aimed to utilize network pharmacology and molecular docking technology to elucidate the molecular mechanisms of action of HQGZWWD in DVT. METHODS We identified the main chemical components of HQGZWWD by reviewing the literature and using a Traditional Chinese Medicine Systems Pharmacology (TCMSP) database. We used GeneCards and Online Mendelian Inheritance in Man databases to identify the targets of DVT. Herb-disease-gene-target networks using Cytascape 3.8.2 software; a protein-protein interaction (PPI) network was constructed by combining drug and disease targets on the STRING platform. Additionally, we conducted Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. Finally, molecular docking verification of active components and core protein targets was conducted. RESULTS A total of 64 potential targets related to DVT were identified in HQGZWWD, with 41 active components; quercetin, kaempferol, and beta-sitosterol were the most effective compounds. The PPI network analysis revealed that AKT1, IL1B, and IL6 were the most abundant proteins with the highest degree. GO analysis indicated that DVT treatment with HQGZWWD could involve the response to inorganic substances, positive regulation of phosphorylation, plasma membrane protein complexes, and signaling receptor regulator activity. KEGG analysis revealed that the signaling pathways included pathways in cancer, lipid and atherosclerosis, fluid shear stress and atherosclerosis, and the phosphatidylinositol 3-kinases/protein kinase B(PI3K-Akt) and mitogen-activated protein kinase (MAPK) signaling pathways. The molecular docking results indicated that quercetin, kaempferol, and beta-sitosterol exhibited strong binding affinities for AKT1, IL1B, and IL6. CONCLUSION Our study suggests that AKT1, IL1B, and IL6 are promising targets for treating DVT with HQGZWWD. The active components of HQGZWWD likely responsible for its effectiveness against DVT are quercetin, kaempferol, and beta-sitosterol, they may inhibit platelet activation and endothelial cell apoptosis by regulating the PI3K/Akt and MAPK signaling pathways, slowing the progression of DVT.
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Affiliation(s)
- Wei Fan
- Department of Orthopaedics, The Affiliated Hospital of Southwest Medical University, Luzhou, China
- Sichuan Provincial Laboratory of Orthopaedic Engineering, Luzhou, China
| | - Shuangli Lan
- Department of Hepatobiliary Surgery, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Yunkang Yang
- Department of Orthopaedics, The Affiliated Hospital of Southwest Medical University, Luzhou, China.
- Sichuan Provincial Laboratory of Orthopaedic Engineering, Luzhou, China.
| | - Jie Liang
- Department of Orthopaedics, The Affiliated Hospital of Southwest Medical University, Luzhou, China.
- Sichuan Provincial Laboratory of Orthopaedic Engineering, Luzhou, China.
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Xu E, Park S, Calderon J, Cao D, Liang B. In Silico Identification and In Vitro Validation of Repurposed Compounds Targeting the RSV Polymerase. Microorganisms 2023; 11:1608. [PMID: 37375110 DOI: 10.3390/microorganisms11061608] [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: 06/03/2023] [Revised: 06/14/2023] [Accepted: 06/14/2023] [Indexed: 06/29/2023] Open
Abstract
Respiratory Syncytial Virus (RSV) is the top cause of infant hospitalization globally, with no effective treatments available. Researchers have sought small molecules to target the RNA-dependent RNA Polymerase (RdRP) of RSV, which is essential for replication and transcription. Based on the cryo-EM structure of the RSV polymerase, in silico computational analysis including molecular docking and the protein-ligand simulation of a database, including 6554 molecules, is currently undergoing phases 1-4 of clinical trials and has resulted in the top ten repurposed compound candidates against the RSV polymerase, including Micafungin, Totrombopag, and Verubecestat. We performed the same procedure to evaluate 18 small molecules from previous studies and chose the top four compounds for comparison. Among the top identified repurposed compounds, Micafungin, an antifungal medication, showed significant inhibition and binding affinity improvements over current inhibitors such as ALS-8112 and Ribavirin. We also validated Micafungin's inhibition of the RSV RdRP using an in vitro transcription assay. These findings contribute to RSV drug development and hold promise for broad-spectrum antivirals targeting the non-segmented negative-sense (NNS) RNA viral polymerases, including those of rabies (RABV) and Ebola (EBOV).
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Affiliation(s)
- Eric Xu
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Seohyun Park
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Juan Calderon
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Dongdong Cao
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Bo Liang
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
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Schäfer J, Klösgen VJ, Omer EA, Kadioglu O, Mbaveng AT, Kuete V, Hildebrandt A, Efferth T. In Silico and In Vitro Identification of P-Glycoprotein Inhibitors from a Library of 375 Phytochemicals. Int J Mol Sci 2023; 24:10240. [PMID: 37373385 DOI: 10.3390/ijms241210240] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Revised: 06/12/2023] [Accepted: 06/14/2023] [Indexed: 06/29/2023] Open
Abstract
Cancer therapy with clinically established anticancer drugs is frequently hampered by the development of drug resistance of tumors and severe side effects in normal organs and tissues. The demand for powerful, but less toxic, drugs is high. Phytochemicals represent an important reservoir for drug development and frequently exert less toxicity than synthetic drugs. Bioinformatics can accelerate and simplify the highly complex, time-consuming, and expensive drug development process. Here, we analyzed 375 phytochemicals using virtual screenings, molecular docking, and in silico toxicity predictions. Based on these in silico studies, six candidate compounds were further investigated in vitro. Resazurin assays were performed to determine the growth-inhibitory effects towards wild-type CCRF-CEM leukemia cells and their multidrug-resistant, P-glycoprotein (P-gp)-overexpressing subline, CEM/ADR5000. Flow cytometry was used to measure the potential to measure P-gp-mediated doxorubicin transport. Bidwillon A, neobavaisoflavone, coptisine, and z-guggulsterone all showed growth-inhibitory effects and moderate P-gp inhibition, whereas miltirone and chamazulene strongly inhibited tumor cell growth and strongly increased intracellular doxorubicin uptake. Bidwillon A and miltirone were selected for molecular docking to wildtype and mutated P-gp forms in closed and open conformations. The P-gp homology models harbored clinically relevant mutations, i.e., six single missense mutations (F336Y, A718C, Q725A, F728A, M949C, Y953C), three double mutations (Y310A-F728A; F343C-V982C; Y953A-F978A), or one quadruple mutation (Y307C-F728A-Y953A-F978A). The mutants did not show major differences in binding energies compared to wildtypes. Closed P-gp forms generally showed higher binding affinities than open ones. Closed conformations might stabilize the binding, thereby leading to higher binding affinities, while open conformations may favor the release of compounds into the extracellular space. In conclusion, this study described the capability of selected phytochemicals to overcome multidrug resistance.
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Affiliation(s)
- Julia Schäfer
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Staudinger Weg 5, 55128 Mainz, Germany
| | - Vincent Julius Klösgen
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Staudinger Weg 5, 55128 Mainz, Germany
- Institute of Bioinformatics, Johannes Gutenberg University, 55131 Mainz, Germany
| | - Ejlal A Omer
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Staudinger Weg 5, 55128 Mainz, Germany
| | - Onat Kadioglu
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Staudinger Weg 5, 55128 Mainz, Germany
| | - Armelle T Mbaveng
- Department of Biochemistry, Faculty of Science, University of Dschang, Dschang P.O. Box 67, Cameroon
| | - Victor Kuete
- Department of Biochemistry, Faculty of Science, University of Dschang, Dschang P.O. Box 67, Cameroon
| | - Andreas Hildebrandt
- Institute of Bioinformatics, Johannes Gutenberg University, 55131 Mainz, Germany
| | - Thomas Efferth
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Staudinger Weg 5, 55128 Mainz, Germany
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Ouahabi S, Loukili EH, Elbouzidi A, Taibi M, Bouslamti M, Nafidi HA, Salamatullah AM, Saidi N, Bellaouchi R, Addi M, Ramdani M, Bourhia M, Hammouti B. Pharmacological Properties of Chemically Characterized Extracts from Mastic Tree: In Vitro and In Silico Assays. Life (Basel) 2023; 13:1393. [PMID: 37374175 DOI: 10.3390/life13061393] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 06/05/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
The mastic tree, scientifically known as Pistacia lentiscus, which belongs to the Anacardiaceae family, was used in this study. The aim of this research was to analyze the chemical composition of this plant and assess its antioxidant and antibacterial properties using both laboratory experiments and computer simulations through molecular docking, a method that predicts the binding strength of a small molecule to a protein. The soxhlet method (SE) was employed to extract substances from the leaves of P. lentiscus found in the eastern region of Morocco. Hexane and methanol were the solvents used for the extraction process. The n-hexane extract was subjected to gas chromatography-mass spectrometry (GC/MS) to identify its fatty acid content. The methanolic extract underwent high-performance liquid chromatography with a diode-array detector (HPLC-DAD) to determine the presence of phenolic compounds. Antioxidant activity was assessed using the DPPH spectrophotometric test. The findings revealed that the main components in the n-hexane extract were linoleic acid (40.97 ± 0.33%), oleic acid (23.69 ± 0.12%), and palmitic acid (22.83 ± 0.10%). Catechin (37.05 ± 0.15%) was identified as the predominant compound in the methanolic extract through HPLC analysis. The methanolic extract exhibited significant DPPH radical scavenging, with an IC50 value of 0.26 ± 0.14 mg/mL. The antibacterial activity was tested against Staphylococcus aureus, Listeria innocua, and Escherichia coli, while the antifungal activity was evaluated against Geotrichum candidum and Rhodotorula glutinis. The P. lentiscus extract demonstrated notable antimicrobial effects. Additionally, apart from molecular docking, other important factors, such as drug similarity, drug metabolism and distribution within the body, potential adverse effects, and impact on bodily systems, were considered for the substances derived from P. lentiscus. Scientific algorithms, such as Prediction of Activity Spectra for Substances (PASS), Absorption, Distribution, Metabolism, Excretion (ADME), and Pro-Tox II, were utilized for this assessment. The results obtained from this research support the traditional medicinal usage of P. lentiscus and suggest its potential for drug development.
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Affiliation(s)
- Safae Ouahabi
- Laboratory of Applied and Environmental Chemistry (LCAE), Faculty of Sciences, Mohammed First University, B.P. 717, Oujda 60000, Morocco
| | - El Hassania Loukili
- Laboratory of Applied and Environmental Chemistry (LCAE), Faculty of Sciences, Mohammed First University, B.P. 717, Oujda 60000, Morocco
| | - Amine Elbouzidi
- Laboratoire d'Amélioration des Productions Agricoles, Biotechnologie et Environnement (LAPABE), Faculté des Sciences, Université Mohammed Premier, Oujda 60000, Morocco
| | - Mohamed Taibi
- Laboratoire d'Amélioration des Productions Agricoles, Biotechnologie et Environnement (LAPABE), Faculté des Sciences, Université Mohammed Premier, Oujda 60000, Morocco
| | - Mohammed Bouslamti
- Laboratories of Natural Substances, Pharmacology, Environment, Modeling, Health and Quality of Life (SNAMOPEQ), Faculty of Sciences, Sidi Mohamed Ben Abdellah University, Fez 30000, Morocco
| | - Hiba-Allah Nafidi
- Department of Food Science, Faculty of Agricultural and Food Sciences, Laval University, Quebec City, QC G1V 0A6, Canada
| | - Ahmad Mohammad Salamatullah
- Department of Food Science & Nutrition, College of Food and Agricultural Sciences, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia
| | - Nezha Saidi
- Laboratory of Applied and Environmental Chemistry (LCAE), Faculty of Sciences, Mohammed First University, B.P. 717, Oujda 60000, Morocco
| | - Reda Bellaouchi
- Laboratory of Bioresources, Biotechnology, Ethnopharmacology and Health, Faculty of Sciences, Mohammed First University, Boulevard Mohamed VI, B.P. 717, Oujda 60000, Morocco
| | - Mohamed Addi
- Laboratoire d'Amélioration des Productions Agricoles, Biotechnologie et Environnement (LAPABE), Faculté des Sciences, Université Mohammed Premier, Oujda 60000, Morocco
| | - Mohamed Ramdani
- Laboratory of Applied and Environmental Chemistry (LCAE), Faculty of Sciences, Mohammed First University, B.P. 717, Oujda 60000, Morocco
| | - Mohammed Bourhia
- Department of Chemistry and Biochemistry, Faculty of Medicine and Pharmacy, Ibn Zohr University, Laayoune 70000, Morocco
| | - Belkheir Hammouti
- Laboratory of Applied and Environmental Chemistry (LCAE), Faculty of Sciences, Mohammed First University, B.P. 717, Oujda 60000, Morocco
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Tripathi J, Gupta S, Gautam S. Alpha-cadinol as a potential ACE-inhibitory volatile compound identified from Phaseolus vulgaris L. through in vitro and in silico analysis. J Biomol Struct Dyn 2023; 41:3847-3861. [PMID: 35380098 DOI: 10.1080/07391102.2022.2057359] [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: 11/22/2021] [Accepted: 03/20/2022] [Indexed: 10/18/2022]
Abstract
Hypertension is a major risk factor of cardiovascular diseases, which is mainly caused due to over activation of renin-angiotensin system. The angiotensin converting enzyme (ACE), which is involved in formation of angiotensin II from angiotensin I, causes the blood vessels to constrict, in turn leading to hypertension. The current study was initiated to understand the role of bioactive volatile compounds from Phaseolus vulgaris L. (common bean), in ACE enzyme inhibition. Beans aqueous extract (BAE) showed maximum ACE inhibition of 88.4 ± 0.8% in comparison to other commonly consumed vegetables like spinach and garlic. The head space gas chromatography-mass spectrometry analysis showed the presence of a number of terpenes and terpenoids, which were present prominently in BAE. In silico molecular docking studies indicated that among the other volatile compounds, alpha-cadinol (-7.27 kcal/mol) and ar-tumerone (-6.44 kcal/mol) have the maximum binding affinity with the active site of ACE, as compared to that of captopril (-6.41 kcal/mol). The molecular dynamic simulation in biological environment, showed that alpha-cadinol forms a stable complex with ACE, with average binding energy of -42 kJ/mol. The ACE:alpha-cadinol complex was found to be stable mainly due to the hydrophobic interactions of alpha-cadinol with active site residues (Tyr523 and Phe457) of ACE. The in silico drug-likeness analysis showed that alpha-cadinol is appropriate for human system with no predicted hepatotoxicity or mutagenicity (AMES toxicity).Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jyoti Tripathi
- Food Technology Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Sumit Gupta
- Food Technology Division, Bhabha Atomic Research Centre, Mumbai, India
| | - Satyendra Gautam
- Food Technology Division, Bhabha Atomic Research Centre, Mumbai, India
- Homi Bhabha National Institute, Anushaktinagar, Mumbai, India
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Ramlal A, Bhat I, Nautiyal A, Baweja P, Mehta S, Kumar V, Tripathi S, Mahto RK, Saini M, Mallikarjuna BP, Saluja S, Lal SK, Subramaniam S, Fawzy IM, Rajendran A. In silico analysis of angiotensin-converting enzyme inhibitory compounds obtained from soybean [ Glycine max (L.) Merr.]. Front Physiol 2023; 14:1172684. [PMID: 37324400 PMCID: PMC10264776 DOI: 10.3389/fphys.2023.1172684] [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: 02/23/2023] [Accepted: 05/02/2023] [Indexed: 06/17/2023] Open
Abstract
Cardiovascular diseases (CVDs) are one of the major reasons for deaths globally. The renin-angiotensin-aldosterone system (RAAS) regulates body hypertension and fluid balance which causes CVD. Angiotensin-converting enzyme I (ACE I) is the central Zn-metallopeptidase component of the RAAS playing a crucial role in maintaining homeostasis of the cardiovascular system. The available drugs to treat CVD have many side effects, and thus, there is a need to explore phytocompounds and peptides to be utilized as alternative therapies. Soybean is a unique legume cum oilseed crop with an enriched source of proteins. Soybean extracts serve as a primary ingredient in many drug formulations against diabetes, obesity, and spinal cord-related disorders. Soy proteins and their products act against ACE I which may provide a new scope for the identification of potential scaffolds that can help in the design of safer and natural cardiovascular therapies. In this study, the molecular basis for selective inhibition of 34 soy phytomolecules (especially of beta-sitosterol, soyasaponin I, soyasaponin II, soyasaponin II methyl ester, dehydrosoyasaponin I, and phytic acid) was evaluated using in silico molecular docking approaches and dynamic simulations. Our results indicate that amongst the compounds, beta-sitosterol exhibited a potential inhibitory action against ACE I.
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Affiliation(s)
- Ayyagari Ramlal
- Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), Pusa Campus, New Delhi, India
- School of Biological Sciences, Universiti Sains Malaysia (USM), Georgetown, Penang, Malaysia
| | - Isha Bhat
- Department of Biosciences, Jamia Millia Islamia, New Delhi, Delhi, India
| | - Aparna Nautiyal
- Department of Botany, Deshbandhu College, University of Delhi, New Delhi, India
| | - Pooja Baweja
- Department of Botany, Maitreyi College, University of Delhi, New Delhi, India
| | - Sahil Mehta
- Department of Botany, Hansraj College, University of Delhi, New Delhi, India
| | - Vikash Kumar
- Faculty of Agricultural Sciences, Institute of Applied Sciences and Humanities, GLA University, Mathura, Uttar Pradesh, India
| | - Shikha Tripathi
- ICAR- National Institute for Biotechnology, New Delhi, India
- Department of Botany, Institute of Science, Banaras Hindu University (BHU), Varanasi, Uttar Pradesh, India
| | - Rohit Kumar Mahto
- Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), Pusa Campus, New Delhi, India
- School of Biotechnology, Institute of Science, Banaras Hindu University (BHU), Varanasi, Uttar Pradesh, India
| | - Manisha Saini
- Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), Pusa Campus, New Delhi, India
| | - Bingi Pujari Mallikarjuna
- Division of Genetics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute (IARI), Regional Research Centre, Dharwad, Karnataka, India
| | - Shukla Saluja
- Department of Botany, Sri Venkateswara College, University of Delhi, New Delhi, India
| | - S. K. Lal
- Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), Pusa Campus, New Delhi, India
| | - Sreeramanan Subramaniam
- School of Biological Sciences, Universiti Sains Malaysia (USM), Georgetown, Penang, Malaysia
- Chemical Centre Biology (CCB), Universiti Sains Malaysia (USM), Bayan Lepas, Penang, Malaysia
- Institute of Nano Optoelectronics Research and Technology, Universiti Sains Malaysia (USM), Bayan Lepas, Penang, Malaysia
| | - Iten M. Fawzy
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Future University in Egypt, Cairo, Egypt
| | - Ambika Rajendran
- Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), Pusa Campus, New Delhi, India
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Bassani D, Moro S. Past, Present, and Future Perspectives on Computer-Aided Drug Design Methodologies. Molecules 2023; 28:molecules28093906. [PMID: 37175316 PMCID: PMC10180087 DOI: 10.3390/molecules28093906] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 04/28/2023] [Accepted: 05/02/2023] [Indexed: 05/15/2023] Open
Abstract
The application of computational approaches in drug discovery has been consolidated in the last decades. These families of techniques are usually grouped under the common name of "computer-aided drug design" (CADD), and they now constitute one of the pillars in the pharmaceutical discovery pipelines in many academic and industrial environments. Their implementation has been demonstrated to tremendously improve the speed of the early discovery steps, allowing for the proficient and rational choice of proper compounds for a desired therapeutic need among the extreme vastness of the drug-like chemical space. Moreover, the application of CADD approaches allows the rationalization of biochemical and interactive processes of pharmaceutical interest at the molecular level. Because of this, computational tools are now extensively used also in the field of rational 3D design and optimization of chemical entities starting from the structural information of the targets, which can be experimentally resolved or can also be obtained with other computer-based techniques. In this work, we revised the state-of-the-art computer-aided drug design methods, focusing on their application in different scenarios of pharmaceutical and biological interest, not only highlighting their great potential and their benefits, but also discussing their actual limitations and eventual weaknesses. This work can be considered a brief overview of computational methods for drug discovery.
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Affiliation(s)
- Davide Bassani
- Pharmaceutical Research & Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., 4070 Basel, Switzerland
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Marzolo 5, 35131 Padova, Italy
| | - Stefano Moro
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Marzolo 5, 35131 Padova, Italy
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Xing H, Wang P, Yan X, Yang Y, Li X, Liu R, Zhou Z. Thermostability enhancement of Escherichia coli phytase by error-prone polymerase chain reaction (epPCR) and site-directed mutagenesis. Front Bioeng Biotechnol 2023; 11:1167530. [PMID: 37064242 PMCID: PMC10101328 DOI: 10.3389/fbioe.2023.1167530] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 03/20/2023] [Indexed: 03/31/2023] Open
Abstract
Phytase efficiently hydrolyzes phytate to phosphate; thus, it is widely used to increase phosphorus availability in animal feeds and reduce phosphorus pollution through excretion. Phytase is easily inactivated during feed pelleting at high temperature, and sufficient thermostability of phytase is essential for industrial applications. In this study, directed evolution was performed to enhance phytase thermostability. Variants were initially expressed in Escherichia coli BL21 for screening, then in Pichia pastoris for characterization. Over 19,000 clones were generated from an error-prone Polymerase Chain Reaction (epPCR) library; 5 mutants (G10, D7, E3, F8, and F9) were obtained with approximately 9.6%, 10.6%, 11.5%, 11.6%, and 12.2% higher residual activities than the parent after treatment at 99°C for 60 min. Three of these mutants, D7, E3, and F8, exhibited 79.8%, 73.2%, and 92.6% increases in catalytic efficiency (kcat/Km), respectively. In addition, the specific activities of D7, E3, and F8 were 2.33-, 1.98-, and 2.02-fold higher than parental phytase; they were also higher than the activities of all known thermostable phytases. Sequence analysis revealed that all mutants were substituted at residue 75 and was confirmed that the substitution of cysteine at position 75 was the main contribution to the improvement of thermostability of mutants by saturation mutagenesis, indicating that this amino acid is crucial for the stability and catalytic efficiency of phytase. Docking structure analysis revealed that substitution of the C75 residue allowed the mutants to form additional hydrogen bonds in the active pocket, thereby facilitating binding to the substrate. In addition, we confirmed that the intrinsic C77-C108 disulfide bond in E. coli phytase is detrimental to its stability.
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Affiliation(s)
- Hongguan Xing
- School of Pharmacy, East China University of Science and Technology, Shanghai, China
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Pingping Wang
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Xing Yan
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Yi Yang
- School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Xinliang Li
- CJ Youtell (Shanghai) Biotech Co., Ltd., Shanghai, China
| | - Rui Liu
- CJ Youtell (Shanghai) Biotech Co., Ltd., Shanghai, China
| | - Zhihua Zhou
- School of Pharmacy, East China University of Science and Technology, Shanghai, China
- CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- *Correspondence: Zhihua Zhou,
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Taibi M, Elbouzidi A, Ou-Yahia D, Dalli M, Bellaouchi R, Tikent A, Roubi M, Gseyra N, Asehraou A, Hano C, Addi M, El Guerrouj B, Chaabane K. Assessment of the Antioxidant and Antimicrobial Potential of Ptychotis verticillata Duby Essential Oil from Eastern Morocco: An In Vitro and In Silico Analysis. Antibiotics (Basel) 2023; 12:antibiotics12040655. [PMID: 37107017 PMCID: PMC10135233 DOI: 10.3390/antibiotics12040655] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 03/23/2023] [Accepted: 03/25/2023] [Indexed: 03/29/2023] Open
Abstract
Ptychotis verticillata Duby, referred to as Nûnkha in the local language, is a medicinal plant that is native to Morocco. This particular plant is a member of the Apiaceae family and has a longstanding history in traditional medicine and has been utilized for therapeutic purposes by practitioners for generations. The goal of this research is to uncover the phytochemical makeup of the essential oil extracted from P. verticillata, which is indigenous to the Touissite region in Eastern Morocco. The extraction of the essential oil of P. verticillata (PVEO) was accomplished through the use of hydro-distillation via a Clevenger apparatus. The chemical profile of the essential oil was then determined through analysis utilizing gas chromatography–mass spectrometry (GC/MS). The study findings indicated that the essential oil of P. verticillata is composed primarily of Carvacrol (37.05%), D-Limonene (22.97%), γ-Terpinene (15.97%), m-Cymene (12.14%) and Thymol (8.49%). The in vitro antioxidant potential of PVEO was evaluated using two methods: the 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical trapping assay and the ferric reducing antioxidant power (FRAP) method. The data demonstrated considerable radical scavenging and relative antioxidative power. Escherichia coli, Staphylococcus aureus, Listeria innocua, and Pseudomonas aeruginosa were the most susceptible bacterial strains tested, while Geotrichum candidum, Candida albicans, and Rhodotorula glutinis were the most resilient fungi strains. PVEO had broad-spectrum antifungal and antibacterial properties. To elucidate the antioxidative and antibacterial characteristics of the identified molecules, we applied the methodology of molecular docking, a computational approach that forecasts the binding of a small molecule to a protein. Additionally, we utilized the Prediction of Activity Spectra for Substances (PASS) algorithm; Absorption, Distribution, Metabolism, and Excretion (ADME); and Pro-Tox II (to predict the toxicity in silico) tests to demonstrate PVEO’s identified compounds’ drug-likeness, pharmacokinetic properties, the anticipated safety features after ingestion, and the potential pharmacological activity. Finally, our findings scientifically confirm the ethnomedicinal usage and usefulness of this plant, which may be a promising source for future pharmaceutical development.
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Affiliation(s)
- Mohamed Taibi
- Laboratoire d’Amélioration des Productions Agricoles, Biotechnologie et Environnement (LAPABE), Faculté des Sciences, Université Mohammed Premier, Oujda 60000, Morocco
- Centre de l’Oriental des Sciences et Technologies de l’Eau et de l’Environnement (COSTEE), Université Mohammed Premier, Oujda 60000, Morocco
| | - Amine Elbouzidi
- Laboratoire d’Amélioration des Productions Agricoles, Biotechnologie et Environnement (LAPABE), Faculté des Sciences, Université Mohammed Premier, Oujda 60000, Morocco
| | - Douaae Ou-Yahia
- Centre de l’Oriental des Sciences et Technologies de l’Eau et de l’Environnement (COSTEE), Université Mohammed Premier, Oujda 60000, Morocco
| | - Mohammed Dalli
- Laboratory of Bioresources, Biotechnology, Ethnopharmacology and Health, Faculty of Sciences, Mohammed First University, Boulevard Mohamed VI, B.P. 717, Oujda 60000, Morocco
- Laboratory of Microbiology, Faculty of Medicine and Pharmacy, University Mohammed The First, Oujda 60000, Morocco
| | - Reda Bellaouchi
- Laboratory of Bioresources, Biotechnology, Ethnopharmacology and Health, Faculty of Sciences, Mohammed First University, Boulevard Mohamed VI, B.P. 717, Oujda 60000, Morocco
| | - Aziz Tikent
- Laboratoire d’Amélioration des Productions Agricoles, Biotechnologie et Environnement (LAPABE), Faculté des Sciences, Université Mohammed Premier, Oujda 60000, Morocco
| | - Mohammed Roubi
- Laboratory of Bioresources, Biotechnology, Ethnopharmacology and Health, Faculty of Sciences, Mohammed First University, Boulevard Mohamed VI, B.P. 717, Oujda 60000, Morocco
| | - Nadia Gseyra
- Laboratory of Bioresources, Biotechnology, Ethnopharmacology and Health, Faculty of Sciences, Mohammed First University, Boulevard Mohamed VI, B.P. 717, Oujda 60000, Morocco
| | - Abdeslam Asehraou
- Laboratory of Bioresources, Biotechnology, Ethnopharmacology and Health, Faculty of Sciences, Mohammed First University, Boulevard Mohamed VI, B.P. 717, Oujda 60000, Morocco
| | - Christophe Hano
- Laboratoire de Biologie des Ligneux et des Grandes Cultures, INRAE USC1328, University of Orleans, CEDEX 2, 45067 Orléans, France
- Correspondence: (C.H.); (M.A.)
| | - Mohamed Addi
- Laboratoire d’Amélioration des Productions Agricoles, Biotechnologie et Environnement (LAPABE), Faculté des Sciences, Université Mohammed Premier, Oujda 60000, Morocco
- Correspondence: (C.H.); (M.A.)
| | - Bouchra El Guerrouj
- Laboratoire d’Amélioration des Productions Agricoles, Biotechnologie et Environnement (LAPABE), Faculté des Sciences, Université Mohammed Premier, Oujda 60000, Morocco
- Centre de l’Oriental des Sciences et Technologies de l’Eau et de l’Environnement (COSTEE), Université Mohammed Premier, Oujda 60000, Morocco
| | - Khalid Chaabane
- Laboratoire d’Amélioration des Productions Agricoles, Biotechnologie et Environnement (LAPABE), Faculté des Sciences, Université Mohammed Premier, Oujda 60000, Morocco
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Diabate O, Cisse C, Sangare M, Soremekun O, Fatumo S, Shaffer JG, Doumbia S, Wele M. Identification of promising high-affinity inhibitors of SARS-CoV-2 main protease from African Natural Products Databases by Virtual Screening. RESEARCH SQUARE 2023:rs.3.rs-2673755. [PMID: 36993208 PMCID: PMC10055610 DOI: 10.21203/rs.3.rs-2673755/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
With the rapid spread of the new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the pathogen agent of COVID-19 pandemic created a serious threat to global public health, requiring the most urgent research for potential therapeutic agents. The availability of genomic data of SARS-CoV-2 and efforts to determine the protein structure of the virus facilitated the identification of potent inhibitors by using structure-based approach and bioinformatics tools. Many pharmaceuticals have been proposed for the treatment of COVID-19, although their effectiveness has not been assessed yet. However, it is important to find out new-targeted drugs to overcome the resistance concern. Several viral proteins such as proteases, polymerases or structural proteins have been considered as potential therapeutic targets. But the virus target must be essential for host invasion match some drugability criterion. In this Work, we selected the highly validated pharmacological target main protease Mpro and we performed high throughput virtual screening of African Natural Products Databases such as NANPDB, EANPDB, AfroDb, and SANCDB to identify the most potent inhibitors with the best pharmacological properties. In total, 8753 natural compounds were virtually screened by AutoDock vina against the main protease of SARS-CoV-2. Two hundred and five (205) compounds showed high-affinity scores (less than - 10.0 Kcal/mol), while fifty-eight (58) filtered through Lipinski's rules showed better affinity than known Mpro inhibitors (i.e., ABBV-744, Onalespib, Daunorubicin, Alpha-ketoamide, Perampanel, Carprefen, Celecoxib, Alprazolam, Trovafloxacin, Sarafloxacin, Ethyl biscoumacetate…). Those promising compounds could be considered for further investigations toward the developpement of SARS-CoV-2 drug development.
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Affiliation(s)
- Oudou Diabate
- University of Sciences, Technics and Technologies of Bamako (USTTB)
| | - Cheickna Cisse
- University of Sciences, Technics and Technologies of Bamako (USTTB)
| | | | | | - Segun Fatumo
- University of Sciences, Technics and Technologies of Bamako (USTTB)
| | | | - Seydou Doumbia
- University of Sciences, Technics and Technologies of Bamako (USTTB)
| | - Mamadou Wele
- University of Sciences, Technics and Technologies of Bamako (USTTB)
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Ramkumar S, Ramarajan R. Design, Synthesis, Spectral Characterization, Antioxidant Activity, Molecular Docking and in silico ADMET Studies of 1, 3 Oxazepines. ChemistrySelect 2023. [DOI: 10.1002/slct.202204818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Affiliation(s)
- Subramaniyan Ramkumar
- Department of Chemistry Annamalai University, Annamalai Nagar Tamil Nadu 608 002 India
| | - Rajalakshmi Ramarajan
- Department of Chemistry Annamalai University, Annamalai Nagar Tamil Nadu 608 002 India
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Tripathi J, Saxena S, Gautam S. Simulation study to assess the effectiveness of gamma radiation for inactivation of viruses on food packaging material. Radiat Phys Chem Oxf Engl 1993 2023; 204:110678. [PMCID: PMC9709647 DOI: 10.1016/j.radphyschem.2022.110678] [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: 03/16/2022] [Revised: 11/25/2022] [Accepted: 11/26/2022] [Indexed: 12/05/2022]
Abstract
The recent COVID-19 pandemic spread across the globe has raised the concern about the possible transmission of viruses through food packaging material during domestic and international trade. Therefore, mitigation strategies are needed to address these safety issues. Preliminary in-silico study showed that interactions between food packaging material and viral surface proteins were possibly hydrophobic in nature with most favourable interaction having a binding free energy of −5.24 kcal/mol. Since these interactions can cause viruses to adsorb on the food packets and get transmitted during supply chain, it is necessary to inactivate the viruses. In this context, efficacy of gamma irradiation in inactivating the viruses on the food packaging material was assessed. For this simulation study P1 (virulent) bacteriophage of E. coli was used as a model system. Gamma irradiation of food packets at an absorbed dose >8 kGy was found to completely inactivate the infectivity of P1(virulent) bacteriophage when co-cultured with E. coli host and assayed for viral plaque formation. Reduction in infectivity of P1(vir) phage was more prominent at ambient temperature (25 ± 2 °C) as compared to cold temperature (6 ± 2 °C) when assayed after storage (one week). Gamma irradiation (2 kGy) completely inactivated the virus particles on food packets when stored for 1 week at both the above temperatures. It is thus proposed that gamma irradiation (2 kGy) can possibly be integrated as a final treatment of the packaged food products to rule out the possibility of viral transmission. However, the efficacy of radiation processing against different pathogenic viruses needs to be determined prior to actual commercial deployment.
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Affiliation(s)
- Jyoti Tripathi
- Food Technology Division, Bhabha Atomic Research Centre, Mumbai, 400085, India
| | - Sudhanshu Saxena
- Food Technology Division, Bhabha Atomic Research Centre, Mumbai, 400085, India
| | - Satyendra Gautam
- Food Technology Division, Bhabha Atomic Research Centre, Mumbai, 400085, India,Homi Bhabha National Institute, Anushaktinagar, Mumbai, 400094, India,Corresponding author. Food Technology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085, Maharashtra, India
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50
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Yu Y, Xu S, He R, Liang G. Application of Molecular Simulation Methods in Food Science: Status and Prospects. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:2684-2703. [PMID: 36719790 DOI: 10.1021/acs.jafc.2c06789] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Molecular simulation methods, such as molecular docking, molecular dynamic (MD) simulation, and quantum chemical (QC) calculation, have become popular as characterization and/or virtual screening tools because they can visually display interaction details that in vitro experiments can not capture and quickly screen bioactive compounds from large databases with millions of molecules. Currently, interdisciplinary research has expanded molecular simulation technology from computer aided drug design (CADD) to food science. More food scientists are supporting their hypotheses/results with this technology. To understand better the use of molecular simulation methods, it is necessary to systematically summarize the latest applications and usage trends of molecular simulation methods in the research field of food science. However, this type of review article is rare. To bridge this gap, we have comprehensively summarized the principle, combination usage, and application of molecular simulation methods in food science. We also analyzed the limitations and future trends and offered valuable strategies with the latest technologies to help food scientists use molecular simulation methods.
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Affiliation(s)
- Yuandong Yu
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing400030, China
| | - Shiqi Xu
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing400030, China
| | - Ran He
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing400030, China
| | - Guizhao Liang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing400030, China
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