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Mazumder K, Aktar A, Kerr PG, Dash R, Blanchard CL, Gulzarul Aziz M, Farahnaky A. Insights into seed coats of nine cultivars of Australian lupin: Unravelling LC-QTOF MS-based biochemical profiles, nutritional, functional, antioxidant, and antidiabetic properties together with rationalizing antidiabetic mechanism by in silico approaches. Food Res Int 2024; 195:114970. [PMID: 39277267 DOI: 10.1016/j.foodres.2024.114970] [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: 04/09/2024] [Revised: 08/12/2024] [Accepted: 08/20/2024] [Indexed: 09/17/2024]
Abstract
Lupins, and other legumes, have attained international interest due to their reported remarkable health benefits. Currently, the seed coats are discarded as waste or animal feed. The research presented here summarizes the potential for incorporating the seed coats into 'whole grain' foods. We aimed to identify metabolites found in the seed coats of nine commercial Australian cultivars of lupin (Lupinus angustifolius and L. albus species), and to evaluate and compare their functional, nutritional, antioxidant, and antidiabetic properties, along with in silico exploration of mechanisms of action for selected identified secondary metabolites. The seed coats were found to contain 79 to 90% dietary fibers and substantial quantity of essential macrometals. LC-QTOF MS-based, untargeted bioactive metabolite profiling explored a total of 673 chemical entities, and identified 63 bioactive secondary metabolites including: biophenols, unsaturated fatty acids, triterpenoids, alkaloids, and dietary prebiotics (insoluble fibers). The seed coats from these nine cultivars show substantial antioxidant activity. The cultivars of L. angustifolius inhibit α-amylase and α-glucosidase significantly in vitro. Moreover, in silico docking and dynamic simulation along with ADME/T analysis suggest that quercetin 3-methyl ether and 8-C-methylquercetin 3-methyl ether as molecules, novel in lupin seed coats, are responsible for the α-amylase and α-glucosidase inhibition. The findings indicated that lupin seed coats might be beneficial food components, rather than be discarded as 'mill waste'.
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Affiliation(s)
- Kishor Mazumder
- Department of Pharmacy, Jashore University of Science and Technology, Jashore, 7408 Jashore, Bangladesh; School of Optometry and Vision Science, UNSW Medicine, University of New South Wales (UNSW), Sydney, NSW, Australia.
| | - Asma Aktar
- Department of Pharmacy, Jashore University of Science and Technology, Jashore, 7408 Jashore, Bangladesh
| | - Philip G Kerr
- School of Dentistry and Medical Sciences, Charles Sturt University, Boorooma St, Wagga Wagga, NSW 2678, Australia
| | - Raju Dash
- Department of Anatomy, Dongguk University College of Medicine, Gyeongju 38066, Republic of Korea
| | - Christopher L Blanchard
- School of Dentistry and Medical Sciences, Charles Sturt University, Boorooma St, Wagga Wagga, NSW 2678, Australia
| | - Mohammad Gulzarul Aziz
- Department of Food Technology and Rural Industries, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Asgar Farahnaky
- Biosciences and Food Technology, School of Science, RMIT University, Melbourne 3083, Australia
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Mosoh DA. Widely-targeted in silico and in vitro evaluation of veratrum alkaloid analogs as FAK inhibitors and dual targeting of FAK and Hh/SMO pathways for cancer therapy: A critical analysis. Int J Biol Macromol 2024:136201. [PMID: 39368576 DOI: 10.1016/j.ijbiomac.2024.136201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2024] [Revised: 09/26/2024] [Accepted: 09/29/2024] [Indexed: 10/07/2024]
Abstract
Focal Adhesive Kinase (FAK), a key player in aggressive cancers, mediates signals crucial for progression, invasion, and metastasis. Despite advances in targeted therapies, drug resistance is still a challenge, and survival rates remain low, particularly for late-stage patients, emphasizing the need for innovative cancer therapeutics. Cyclopamine, a veratrum alkaloid, has shown promising anti-tumor properties, but the search for more potent analogs with enhanced affinity for the biological target continues. This study employs a hybrid virtual screening approach combining pharmacophore model-based virtual screening (PB-VS) and docking-based virtual screening (DB-VS) to identify potential inhibitors of the FAK catalytic domain. PB-VS on the PubChem database yielded a set of hits, which were then docked with the FAK catalytic domain in two stages (1st and 2nd DB-VS). Hits were ranked based on docking scores and interactions with the active site. The top three compounds underwent molecular dynamics simulations, alongside two control compounds (SMO inhibitor(s) and FAK inhibitor(s)), to assess stability through RMSD, RMSF, Rg, and SASA analyses. ADMET properties were evaluated, and compounds were filtered based on drug-likeness criteria. Molecular dynamics simulations demonstrated the stability of compounds when complexed with the FAK catalytic domain. Compounds 16 (-25 kcal/mol), 88 (-27.47 kcal/mol), and 87 (-18.94 kcal/mol) exhibited comparable docking scores, interaction profiles, stability, and binding energies, indicating their potential as lead candidates. However, further validation and optimization through quantitative structure-activity relationship (QSAR) studies are essential to refine their efficacy and therapeutic potential. The in vitro cell-based assay demonstrated that compound 101PF, a FAK inhibitor, significantly inhibited the proliferation and migration of A549 cells. However, the results regarding the combined effects of FAK and SMO inhibitors were inconclusive, highlighting the need for further investigation. This study contributes to developing more effective anti-cancer drugs by improving the understanding of potential cyclopamine-based veratrum alkaloid analogs with enhanced interactions with the FAK catalytic domain.
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Affiliation(s)
- Dexter Achu Mosoh
- Centre for Biodiversity Exploration and Conservation (CBEC), 15, Kundan Residency, 4th Mile Mandla Road, Tilhari, Jabalpur, M.P 482021, India; Indian Institute of Technology Gandhinagar, Palaj Campus, Gujarat 382355, India; School of Science, Sanjeev Agrawal Global Educational (SAGE) University, Bhopal, M.P 462022, India; Prof. Wagner A. Vendrame's Laboratory, Environmental Horticulture Department, University of Florida, Institute of Food and Agricultural Sciences, 2550 Hull Rd., Gainesville, FL 32611, USA.
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Chen J, Wang J, Yang W, Zhao L, Hu G. Conformations of KRAS4B Affected by Its Partner Binding and G12C Mutation: Insights from GaMD Trajectory-Image Transformation-Based Deep Learning. J Chem Inf Model 2024; 64:6880-6898. [PMID: 39197061 DOI: 10.1021/acs.jcim.4c01174] [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: 08/30/2024]
Abstract
Binding of partners and mutations highly affects the conformational dynamics of KRAS4B, which is of significance for deeply understanding its function. Gaussian accelerated molecular dynamics (GaMD) simulations followed by deep learning (DL) and principal component analysis (PCA) were carried out to probe the effect of G12C and binding of three partners NF1, RAF1, and SOS1 on the conformation alterations of KRAS4B. DL reveals that G12C and binding of partners result in alterations in the contacts of key structure domains, such as the switch domains SW1 and SW2 together with the loops L4, L5, and P-loop. Binding of NF1, RAF1, and SOS1 constrains the structural fluctuation of SW1, SW2, L4, and L5; on the contrary, G12C leads to the instability of these four structure domains. The analyses of free energy landscapes (FELs) and PCA also show that binding of partners maintains the stability of the conformational states of KRAS4B while G12C induces greater mobility of the switch domains SW1 and SW2, which produces significant impacts on the interactions of GTP with SW1, L4, and L5. Our findings suggest that partner binding and G12C play important roles in the activity and allosteric regulation of KRAS4B, which may theoretically aid in further understanding the function of KRAS4B.
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Affiliation(s)
- Jianzhong Chen
- School of Science, Shandong Jiaotong University, Jinan 250357, China
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
| | - Jian Wang
- School of Science, Shandong Jiaotong University, Jinan 250357, China
| | - Wanchun Yang
- School of Science, Shandong Jiaotong University, Jinan 250357, China
| | - Lu Zhao
- School of Science, Shandong Jiaotong University, Jinan 250357, China
| | - Guodong Hu
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
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Wang R, Duan L, Zhao B, Zheng Y, Chen L. Molecular recognition between volatile molecules and odorant binding proteins 7 by homology modeling, molecular docking and molecular dynamics simulation. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2024; 104:7592-7602. [PMID: 38767431 DOI: 10.1002/jsfa.13595] [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: 02/27/2024] [Revised: 05/01/2024] [Accepted: 05/04/2024] [Indexed: 05/22/2024]
Abstract
BACKGROUND Odorant-binding proteins (OBPs) in insects are key to detection and recognition of external chemical signals associated with survival. OBP7 in Spodoptera frugiperda's larval stage (SfruOBP7) may search for host plants by sensing plant volatiles, which are important sources of pest attractants and repellents. However, the atomic-level basis of binding modes remains elusive. RESULTS SfruOBP7 structure was constructed through homology modeling, and complex models of six plant volatiles ((E)-2-hexenol, α-pinene, (Z)-3-hexenyl acetate, lauric acid, O-cymene and 1-octanol) and SfruOBP7 were obtained through molecular docking. To study the detailed interactions between the six plant volatile molecules and SfruOBP7, we conducted three 300 ns molecular dynamics simulations for each study object. The correlation coefficients between binding free energy obtained by molecular mechanics/generalized Born surface area together with solvated interaction energy methods and experimental values are 0.90 and 0.88, respectively, showing a good correlation. By comparing binding free energy along with interaction patterns between SfruOBP7 and the six volatile molecules, hotspot residues of SfruOBP7 when binding with different volatile molecules were determined. Hydrophobic interactions stemming from van der Waals interactions play a significant role in SfruOBP7 and these plant volatile systems. CONCLUSION The optimized three-dimensional structure of SfruOBP7 and its binding modes with six plant volatiles revealed their interactions, thus providing a means for estimating the binding energies of other plant volatiles. Our study will help to guide the rational design of effective and selective insect attractants. © 2024 Society of Chemical Industry.
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Affiliation(s)
- Ruige Wang
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar, China
| | - Lixin Duan
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar, China
| | - Bing Zhao
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar, China
- Heilongjiang Provincial Key Laboratory of Surface Active Agent and Auxiliary, Qiqihar University, Qiqihar, China
| | - Yongjie Zheng
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar, China
| | - Lin Chen
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar, China
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Akinjiyan MO, Elekofehinti OO, Oluwatuyi AO, Nwanna EE, Lawal AO. Investigation of Cissus populnea as a Potential Therapeutic Agent for Erectile Dysfunction. Cell Biochem Biophys 2024:10.1007/s12013-024-01486-4. [PMID: 39217270 DOI: 10.1007/s12013-024-01486-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/09/2024] [Indexed: 09/04/2024]
Abstract
Cissus populnea (CP) is a plant reported to possess an erection-enhancing ability, though mechanisms remain unclear. Drugs targeting phosphodiesterase 5 (PDE5) inhibition, such as sildenafil, have been employed to treat erectile dysfunction (EDRF), but they are associated with several complications. This study investigated the effect of C. populnea extracts (aqueous and saponin-rich) on the activity and gene expressions of proteins related to erection. PDE5, Nitric oxide synthase (NOS) and androgen receptor (AR) genes were studied using RT-PCR on CP-treated paroxetine-induced ERDF-rats. It also employed Schrödinger suites for investigations such as molecular and induced-fit docking, MMGBSA, ADMET, and QSAR profiling of CP-phytocompounds. C. populnea extracts reduce the activity and downregulate the expression of the PDE5 gene while upregulating the expressions of AR and NOS genes in the ERDF-rats relative to the control group. Five (leading) compounds with induced-fit docking (IFD) scores in kcal/mol, namely, stigmasterol (-638.73), daucosterol (-644.73), furostanol (-639.29), papaverine (-639.03), and capsaicin (-642.88), had better docking scores of -9.936, -9.824, -9.064, -8.863, and -8.736 kcal/mol, respectively, compared with those of sildenafil (-8.611 kcal/mol). They also showed an excellent ADMET profile, satisfying Lipinski's rule of five. The MMGBSA predictions revealed that stigmasterol, daucosterol, papaverine, and capsaicin had binding free energies of -45.29, -59.14, -50.63, and -50.47 kcal/mol, respectively, suggesting that they are significant inhibitors of PDE5. The QSAR model revealed that lead compounds possess good pIC50 values. These results indicate that C. populnea is a more promising possible treatment for controlling EDRF and deserves further research.
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Affiliation(s)
- Moses Orimoloye Akinjiyan
- Bioinformatics and Molecular Biology Unit, Department of Biochemistry, Federal University of Technology, Akure, Ondo State, Nigeria.
- Teady Bioscience Research Laboratory, Akure, Ondo State, Nigeria.
| | - Olusola Olalekan Elekofehinti
- Bioinformatics and Molecular Biology Unit, Department of Biochemistry, Federal University of Technology, Akure, Ondo State, Nigeria
- Teady Bioscience Research Laboratory, Akure, Ondo State, Nigeria
| | - Adedotun Olayemi Oluwatuyi
- Bioinformatics and Molecular Biology Unit, Department of Biochemistry, Federal University of Technology, Akure, Ondo State, Nigeria
- Teady Bioscience Research Laboratory, Akure, Ondo State, Nigeria
| | - Esther Emem Nwanna
- Functional foods and Nutrigenomics unit, Department of Biochemistry, Federal University of Technology, Akure, Ondo State, Nigeria
| | - Akeem Olalekan Lawal
- Bioinformatics and Molecular Biology Unit, Department of Biochemistry, Federal University of Technology, Akure, Ondo State, Nigeria
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Xing G, Zheng Q. Insights into the specific feature of the electrostatic recognition binding mechanism between BM2 and BM1: a molecular dynamics simulation study. Phys Chem Chem Phys 2024; 26:22726-22738. [PMID: 39161312 DOI: 10.1039/d4cp01936a] [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: 08/21/2024]
Abstract
Matrix protein 2 (M2) and matrix protein 1 (M1) of the influenza B virus are two important proteins, and the interactions between BM2 and BM1 play an important role in the process of virus assembly and replication. However, the interaction details between BM2 and BM1 are still unclear at the atomic level. Here, we constructed the BM2-BM1 complex system using homology modelling and molecular docking methods. Molecular dynamics (MD) simulations were used to illustrate the binding mechanism between BM2 and BM1. The results identify that the eight polar residues (E88B, E89B, H119BM1, E94B, R101BM1, K102BM1, R105BM1, and E104B) play an important role in stabilizing the binding through the formation of hydrogen bond networks and salt-bridge interactions at the binding interface. Furthermore, based on the simulation results and the experimental facts, the mutation experiments were designed to verify the influence of the mutation of residues both within and outside the effector domain. The mutations directly or indirectly disrupt interactions between polar residues, thus affecting viral assembly and replication. The results could help us understand the details of the interactions between BM2 and BM1 and provide useful information for the anti-influenza drug design.
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Affiliation(s)
- Guixuan Xing
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun 130023, China
| | - Qingchuan Zheng
- School of Pharmaceutical Sciences, Jilin University, Changchun 130021, China.
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun 130023, China
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Zhan J, Liu Z, Gao H. Theoretical study on the design of allosteric inhibitors of diabetes associated protein PTP1B. Front Pharmacol 2024; 15:1423029. [PMID: 39239651 PMCID: PMC11374740 DOI: 10.3389/fphar.2024.1423029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Accepted: 08/05/2024] [Indexed: 09/07/2024] Open
Abstract
The protein tyrosine phosphatase 1B (PTP1B) is a critical therapeutic target for type 2 diabetes mellitus (T2DM). Many PTP1B inhibitors have been reported, however, most of them lack high specificity and have adverse effects. Designing effective PTP1B inhibitors requires understanding the molecular mechanism of action between inhibitors and PTP1B. To this end, molecular dynamics (MD) simulations and molecular mechanics Poisson Boltzmann Surface Area (MM-PB/SA) methods were used to observe the binding patterns of compounds with similar pentacyclic triterpene parent ring structures but different inhibition abilities. Through structure and energy analysis, we found that the positions of cavities and substituents significantly affect combining capacity. Besides, we constructed a series of potential inhibitor molecules using LUDI and rational drug design methods. The ADMET module of Discovery Studio 2020 was used to predict the properties of these inhibitor molecules. Lastly, we obtained compounds with low toxicity and significant inhibitory activity. The study will contribute to the treatment of T2DM.
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Affiliation(s)
- Jiuyu Zhan
- School of Life Science, Ludong University, Yantai, Shandong, China
| | - Zhenyang Liu
- School of Life Science, Ludong University, Yantai, Shandong, China
| | - Hongwei Gao
- School of Life Science, Ludong University, Yantai, Shandong, China
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Wang B, Wang J, Yang W, Zhao L, Wei B, Chen J. Unveiling Allosteric Regulation and Binding Mechanism of BRD9 through Molecular Dynamics Simulations and Markov Modeling. Molecules 2024; 29:3496. [PMID: 39124901 PMCID: PMC11314499 DOI: 10.3390/molecules29153496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2024] [Revised: 07/15/2024] [Accepted: 07/24/2024] [Indexed: 08/12/2024] Open
Abstract
Bromodomain-containing protein 9 (BRD9) is a key player in chromatin remodeling and gene expression regulation, and it is closely associated with the development of various diseases, including cancers. Recent studies have indicated that inhibition of BRD9 may have potential value in the treatment of certain cancers. Molecular dynamics (MD) simulations, Markov modeling and principal component analysis were performed to investigate the binding mechanisms of allosteric inhibitor POJ and orthosteric inhibitor 82I to BRD9 and its allosteric regulation. Our results indicate that binding of these two types of inhibitors induces significant structural changes in the protein, particularly in the formation and dissolution of α-helical regions. Markov flux analysis reveals notable changes occurring in the α-helicity near the ZA loop during the inhibitor binding process. Calculations of binding free energies reveal that the cooperation of orthosteric and allosteric inhibitors affects binding ability of inhibitors to BRD9 and modifies the active sites of orthosteric and allosteric positions. This research is expected to provide new insights into the inhibitory mechanism of 82I and POJ on BRD9 and offers a theoretical foundation for development of cancer treatment strategies targeting BRD9.
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Affiliation(s)
- Bin Wang
- Center for Medical Artificial Intelligence, Shandong University of Traditional Chinese Medicine, Qingdao 266112, China;
| | - Jian Wang
- School of Science, Shandong Jiaotong University, Jinan 250357, China; (J.W.); (W.Y.); (L.Z.)
| | - Wanchun Yang
- School of Science, Shandong Jiaotong University, Jinan 250357, China; (J.W.); (W.Y.); (L.Z.)
| | - Lu Zhao
- School of Science, Shandong Jiaotong University, Jinan 250357, China; (J.W.); (W.Y.); (L.Z.)
| | - Benzheng Wei
- Center for Medical Artificial Intelligence, Shandong University of Traditional Chinese Medicine, Qingdao 266112, China;
| | - Jianzhong Chen
- School of Science, Shandong Jiaotong University, Jinan 250357, China; (J.W.); (W.Y.); (L.Z.)
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Bu F, Chen L, Sun Y, Zhao B, Wang R. Insight into the Binding Interaction between PEDCs and hERRγ Utilizing Molecular Docking and Molecular Dynamics Simulations. Molecules 2024; 29:3256. [PMID: 39064835 PMCID: PMC11278984 DOI: 10.3390/molecules29143256] [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: 05/30/2024] [Revised: 07/03/2024] [Accepted: 07/03/2024] [Indexed: 07/28/2024] Open
Abstract
Phenolic environmental endocrine-disrupting chemicals (PEDCs) are persistent EDCs that are widely found in food packaging materials and environmental media and seriously threaten human health and ecological security. Human estrogen-related receptor γ (hERRγ) has been proposed as a mediator for the low-dose effects of many environmental PEDCs; however, the atomic-level descriptions of dynamical structural features and interactions of hERRγ and PEDCs are still unclarified. Herein, how three PEDCs, 4-(1-methylpropyl)phenol (4-sec-butylphenol), 5,6,7,8-tetrahydro-2-naphthol (tetrahydro-2-napthol), and 2,2-bis(4-hydroxy-3,5-dimethoxyphenyl)propane (BP(2,2)(Me)), interact with hERRγ to produce its estrogenic disruption effects was studied. Molecular docking and multiple molecular dynamics (MD) simulations were first conducted to distinguish the detailed interaction pattern of hERRγ with PEDCs. These binding structures revealed that residues around Leu271, Leu309, Leu345, and Phe435 are important when binding with PEDCs. Furthermore, the binding energies of PEDCs with hERRγ were also characterized using the molecular mechanics/Poisson Boltzmann surface area (MM-PBSA) and solvated interaction energy (SIE) methods, and the results showed that the interactions of CH-π, π-π, and hydrogen bonds are the major contributors for hERRγ binding to these three PEDCs. What is striking is that the methoxide groups of BP(2,2)(Me), as hydrophobic groups, can help to reduce the binding energy of PEDCs binding with hERRγ. These results provide important guidance for further understanding the influence of PEDCs on human health problems.
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Affiliation(s)
- Fanqiang Bu
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar 161006, China; (F.B.); (Y.S.); (B.Z.)
- State Key Laboratory of Organic-Inorganic Composites, Beijing Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing 100029, China
| | - Lin Chen
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar 161006, China; (F.B.); (Y.S.); (B.Z.)
| | - Ying Sun
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar 161006, China; (F.B.); (Y.S.); (B.Z.)
| | - Bing Zhao
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar 161006, China; (F.B.); (Y.S.); (B.Z.)
- Heilongjiang Provincial Key Laboratory of Surface Active Agent and Auxiliary, Qiqihar University, Qiqihar 161006, China
| | - Ruige Wang
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar 161006, China; (F.B.); (Y.S.); (B.Z.)
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Wujieti B, Feng X, Liu E, Li D, Hao M, Zhou L, Cui W. A theoretical study on the activity and selectivity of IDO/TDO inhibitors. Phys Chem Chem Phys 2024; 26:16747-16764. [PMID: 38818624 DOI: 10.1039/d3cp06036e] [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: 06/01/2024]
Abstract
Indoleamine 2,3-dioxygenase 1 (IDO) is a tryptophan (Trp) metabolic enzyme along the kynurenine (NFK) pathway. Under pathological conditions, IDO overexpressed by tumor cells causes depletion of tryptophan and the accumulation of metabolic products, which inhibit the local immune response and form immune escape. Therefore, the suppression of IDO activity is one of the strategies for tumor immunotherapy, and drug design for this target has been the focus of research for more than two decades. Apart from IDO, tryptophan dioxygenase (TDO) of the same family can also catalyze the same biochemical reaction in the human body, but it has different tissue distribution and substrate selectivity from IDO. Based on the principle of drug design with high potency and low cross-reactivity to specific targets, in this subject, the activity and selectivity of IDO and TDO toward small molecular inhibitors were studied from the perspective of thermodynamics and kinetics. The aim was to elucidate the structural requirements for achieving favorable biological activity and selectivity of IDO and TDO inhibitors. Specifically, the interactions of inhibitors from eight families with IDO and TDO were initially investigated through molecular docking and molecular dynamics simulations, and the thermodynamic data for binding of inhibitors were predicted by the molecular mechanics/generalized Born surface area (MM/GBSA) method. Secondly, we explored the free energy landscape of JKloops, the kinetic control element of IDO/TDO, using temperature replica exchange molecular dynamics (T-REMD) simulations and elucidated the connection between the rules of IDO/TDO conformational changes and the inhibitor selectivity mechanism. Furthermore, the binding and dissociation processes of the C1 inhibitor (NLG919) were simulated by the adaptive steering molecular dynamics (ASMD) method, which not only addressed the possible stable, metastable, and transition states for C1 inhibitor-IDO/TDO interactions, but also accurately predicted kinetic data for C1 inhibitor binding and dissociation. In conclusion, we have constructed a complete process from enzyme (IDO/TDO) conformational activation to inhibitor binding/dissociation and used the thermodynamic and kinetic data of each link as clues to verify the control mechanism of IDO/TDO on inhibitor selectivity. This is of great significance for us to understand the design principles of tumor immunotherapy drugs and to avoid drug resistance of immunotherapy drugs.
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Affiliation(s)
- Baerlike Wujieti
- School of Chemical Sciences, University of Chinese Academy of Sciences, No. 19A, YuQuan Road, Beijing 100049, China.
| | - Xinping Feng
- School of Chemical Sciences, University of Chinese Academy of Sciences, No. 19A, YuQuan Road, Beijing 100049, China.
| | - Erxia Liu
- School of Chemical Sciences, University of Chinese Academy of Sciences, No. 19A, YuQuan Road, Beijing 100049, China.
| | - Deqing Li
- School of Chemical Sciences, University of Chinese Academy of Sciences, No. 19A, YuQuan Road, Beijing 100049, China.
| | - Mingtian Hao
- School of Chemical Sciences, University of Chinese Academy of Sciences, No. 19A, YuQuan Road, Beijing 100049, China.
| | - Luqi Zhou
- School of Chemical Sciences, University of Chinese Academy of Sciences, No. 19A, YuQuan Road, Beijing 100049, China.
| | - Wei Cui
- School of Chemical Sciences, University of Chinese Academy of Sciences, No. 19A, YuQuan Road, Beijing 100049, China.
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Zhao L, Wang J, Yang W, Zhao K, Sun Q, Chen J. Unveiling Conformational States of CDK6 Caused by Binding of Vcyclin Protein and Inhibitor by Combining Gaussian Accelerated Molecular Dynamics and Deep Learning. Molecules 2024; 29:2681. [PMID: 38893554 PMCID: PMC11174096 DOI: 10.3390/molecules29112681] [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: 05/08/2024] [Revised: 05/29/2024] [Accepted: 06/03/2024] [Indexed: 06/21/2024] Open
Abstract
CDK6 plays a key role in the regulation of the cell cycle and is considered a crucial target for cancer therapy. In this work, conformational transitions of CDK6 were identified by using Gaussian accelerated molecular dynamics (GaMD), deep learning (DL), and free energy landscapes (FELs). DL finds that the binding pocket as well as the T-loop binding to the Vcyclin protein are involved in obvious differences of conformation contacts. This result suggests that the binding pocket of inhibitors (LQQ and AP9) and the binding interface of CDK6 to the Vcyclin protein play a key role in the function of CDK6. The analyses of FELs reveal that the binding pocket and the T-loop of CDK6 have disordered states. The results from principal component analysis (PCA) indicate that the binding of the Vcyclin protein affects the fluctuation behavior of the T-loop in CDK6. Our QM/MM-GBSA calculations suggest that the binding ability of LQQ to CDK6 is stronger than AP9 with or without the binding of the Vcyclin protein. Interaction networks of inhibitors with CDK6 were analyzed and the results reveal that LQQ contributes more hydrogen binding interactions (HBIs) and hot interaction spots with CDK6. In addition, the binding pocket endures flexibility changes from opening to closing states and the Vcyclin protein plays an important role in the stabilizing conformation of the T-loop. We anticipate that this work could provide useful information for further understanding the function of CDK6 and developing new promising inhibitors targeting CDK6.
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Affiliation(s)
- Lu Zhao
- School of Science, Shandong Jiaotong University, Jinan 250357, China; (J.W.); (W.Y.); (K.Z.); (Q.S.)
| | | | | | | | | | - Jianzhong Chen
- School of Science, Shandong Jiaotong University, Jinan 250357, China; (J.W.); (W.Y.); (K.Z.); (Q.S.)
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12
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Saini S, Pareekh S, Kumar Y. Investigating the structural impact of Omicron RBD mutation on antibody escape and receptor management. J Biomol Struct Dyn 2024; 42:4668-4678. [PMID: 37334729 DOI: 10.1080/07391102.2023.2222174] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 06/01/2023] [Indexed: 06/20/2023]
Abstract
The SARS-CoV-2 Variant B.1.1.5291 evolved rapidly in late November 2021 from the existing mutants sparking fear worldwide owing to its infamous immune escape from a varied class of neutralising antibodies. To assess the structural behaviour of Omicron-Receptor Binding Domain (RBD) upon interacting with cross-reactive CR3022 antibody, we investigated the computational approach of structural engagement in B.1.1529 RBD and wild-type RBD with CR3022 antibody. The current study investigates the interacting interface between the RBDs and CR3022 to decipher the key residues accompanying the potential mutational landscape of SARS-CoV-2 variants. We conducted in-silico docking followed by molecular dynamics simulation analysis to examine the dynamic behaviour of protein-protein interactions. Furthermore, the study unleashed possible interactions post energy decomposition analysis via MM-GBSA. Conclusively, the mutational landscape of RBD eases in designing and discovering the effective neutralisation accompanied by development of a universal vaccine.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Samvedna Saini
- Department of Biological Sciences and Engineering (BSE), Netaji Subhas University of Technology (NSUT), New Delhi, India
| | - Savita Pareekh
- High Performance Computing (HPC) & AI Innovation Lab, Dell EMC, Bengaluru, India
| | - Yatender Kumar
- Department of Biological Sciences and Engineering (BSE), Netaji Subhas University of Technology (NSUT), New Delhi, India
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13
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Yazdani B, Sirous H, Enguita FJ, Brogi S, Wing PAC, Fassihi A. Discovery of novel direct small-molecule inhibitors targeting HIF-2α using structure-based virtual screening, molecular dynamics simulation, and MM-GBSA calculations. Mol Divers 2024; 28:1203-1224. [PMID: 37120484 DOI: 10.1007/s11030-023-10650-6] [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: 11/12/2022] [Accepted: 04/11/2023] [Indexed: 05/01/2023]
Abstract
Hypoxia-inducible factors (HIFs) are the main regulatory factors implicated in the adaptation of cancer cells to hypoxic stress, which has provoked much interest as an attractive target for the design of promising chemotherapeutic agents. Since indirect HIF inhibitors (HIFIs) lead to the occurrence of various side effects, the need of the hour is to develop direct HIFIs, physically interacting with important functional domains within the HIF protein structure. Accordingly, in the present study, it was attempted to develop an exhaustive structure-based virtual screening (VS) process coupled with molecular docking, molecular dynamic (MD) simulation, and MM-GBSA calculations for the identification of novel direct inhibitors against the HIF-2α subunit. For this purpose, a focused library of over 200,000 compounds from the NCI database was used for VS against the PAS-B domain of the target protein, HIF-2α. This domain was suggested to be a possible ligand-binding site, which is characterized by a large internal hydrophobic cavity, unique to the HIF-2α subunit. The top-ranked compounds, NSC106416, NSC217021, NSC217026, NSC215639, and NSC277811 with the best docking scores were taken up for the subsequent in silico ADME properties and PAINS filtration. The selected drug-like hits were employed for carrying out MD simulation which was followed by MM-GBSA calculations to retrieve the candidates showing the highest in silico binding affinity towards the PAS-B domain of HIF-2α. The analysis of results indicated that all molecules, except the NSC277811, fulfilled necessary drug-likeness properties. Four selected drug-like candidates, NSC106416, NSC217021, NSC217026, and NSC215639 were found to expose the stability profiles within the cavity located inside the PAS-B domain of HIF-2α over simulation time. Finally, the results of the MM-GBSA rescoring method were indicative of the highest binding affinity of NSC217026 for the binding site of the HIF-2α PAS-B domain among selected final hits. Consequently, the hit NSC217026 could serve as a promising scaffold for further optimization toward the design of direct HIF-2α inhibitors for cancer therapy.
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Affiliation(s)
- Behnaz Yazdani
- Department of Tissue Engineering, Najafabad Branch, Islamic Azad University, Najafabad, Iran
| | - Hajar Sirous
- Bioinformatics Research Center, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, 81746-73461, Iran.
| | - Francisco J Enguita
- Faculdade de Medicina, Instituto de Medicina Molecular João Lobo Antunes, Universidade de Lisboa, Lisbon, Portugal
| | - Simone Brogi
- Bioinformatics Research Center, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, 81746-73461, Iran.
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126, Pisa, Italy.
| | - Peter A C Wing
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Afshin Fassihi
- Bioinformatics Research Center, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, 81746-73461, Iran
- Department of Medicinal Chemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, 81746-73461, Iran
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14
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Haque S, Ahmad F, Mathkor DM, Makhdoom H, Johargy AK, Faidah H, Babalghith AO, Jalal NA, Alhindi Z, Bantun F. Binding selectivity analysis of new delhi metallo-beta-lactamase-1 inhibitors using molecular dynamics simulations: Exploring possibilities for decoding antimicrobial drug resistance. J Infect Public Health 2024; 17:1108-1116. [PMID: 38714123 DOI: 10.1016/j.jiph.2024.04.018] [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: 02/14/2024] [Revised: 03/25/2024] [Accepted: 04/21/2024] [Indexed: 05/09/2024] Open
Abstract
BACKGROUND New Delhi metallo-beta-lactamase-1 (NDM1) confers resistance to several bacterial species against a broad range of beta-lactam antibiotics and turning them into superbugs that pose a significant threat to healthcare systems worldwide. As such, it is a potentially relevant biological target for counteracting bacterial infections. Given the lack of effective treatment options against NDM1 producing bacteria, finding a reliable inhibitor for the NDM1 enzyme is crucial. METHODS Using molecular dynamics simulations, the binding selectivities and affinities of three ligands, viz. PNK, 3S0, and N1G were investigated against NDM1. RESULTS The results indicate that N1G binds with more affinity to NDM1 than PNK and 3S0. The binding energy decomposition analysis revealed that residues I35, W93, H189, K211, and N220 showed significant binding energies with PNK, 3S0, and N1G, and hence are crucially involved in the binding of the ligands to NDM1. Molecular dynamics trajectory analysis further elicited that the ligands influence dynamic flexibility of NDM1 morphology, which contributes to the partial selectivities of PNK, 3S0, and N1G. CONCLUSIONS This in silico study offers a vital information for developing potential NDM1 inhibitors with high selectivity. Nevertheless, in vitro and in vivo experimental validation is mandated to extend the possible applications of these ligands as NDM1 inhibitors that succor in combating antimicrobial resistance.
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Affiliation(s)
- Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Health Sciences, Jazan University, Jazan 45142, Saudi Arabia; Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut, Lebanon.
| | - Faraz Ahmad
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, India.
| | - Darin Mansor Mathkor
- Research and Scientific Studies Unit, College of Nursing and Health Sciences, Jazan University, Jazan 45142, Saudi Arabia.
| | - Hatim Makhdoom
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taibah University, Madinah, Saudi Arabia.
| | - Ayman K Johargy
- Department of Microbiology and Parasitology, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia.
| | - Hani Faidah
- Department of Microbiology and Parasitology, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia.
| | - Ahmad O Babalghith
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia.
| | - Naif A Jalal
- Department of Microbiology and Parasitology, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia.
| | - Zain Alhindi
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah, Saudi Arabia.
| | - Farkad Bantun
- Department of Microbiology and Parasitology, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia.
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15
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Chen J, Wang J, Yang W, Zhao L, Zhao J, Hu G. Molecular Mechanism of Phosphorylation-Mediated Impacts on the Conformation Dynamics of GTP-Bound KRAS Probed by GaMD Trajectory-Based Deep Learning. Molecules 2024; 29:2317. [PMID: 38792177 PMCID: PMC11123822 DOI: 10.3390/molecules29102317] [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: 04/23/2024] [Revised: 05/09/2024] [Accepted: 05/12/2024] [Indexed: 05/26/2024] Open
Abstract
The phosphorylation of different sites produces a significant effect on the conformational dynamics of KRAS. Gaussian accelerated molecular dynamics (GaMD) simulations were combined with deep learning (DL) to explore the molecular mechanism of the phosphorylation-mediated effect on conformational dynamics of the GTP-bound KRAS. The DL finds that the switch domains are involved in obvious differences in conformation contacts and suggests that the switch domains play a key role in the function of KRAS. The analyses of free energy landscapes (FELs) reveal that the phosphorylation of pY32, pY64, and pY137 leads to more disordered states of the switch domains than the wild-type (WT) KRAS and induces conformational transformations between the closed and open states. The results from principal component analysis (PCA) indicate that principal motions PC1 and PC2 are responsible for the closed and open states of the phosphorylated KRAS. Interaction networks were analyzed and the results verify that the phosphorylation alters interactions of GTP and magnesium ion Mg2+ with the switch domains. It is concluded that the phosphorylation pY32, pY64, and pY137 tune the activity of KRAS through changing conformational dynamics and interactions of the switch domains. We anticipated that this work could provide theoretical aids for deeply understanding the function of KRAS.
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Affiliation(s)
- Jianzhong Chen
- School of Science, Shandong Jiaotong University, Jinan 250357, China; (J.W.); (W.Y.); (L.Z.); (J.Z.)
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
| | - Jian Wang
- School of Science, Shandong Jiaotong University, Jinan 250357, China; (J.W.); (W.Y.); (L.Z.); (J.Z.)
| | - Wanchun Yang
- School of Science, Shandong Jiaotong University, Jinan 250357, China; (J.W.); (W.Y.); (L.Z.); (J.Z.)
| | - Lu Zhao
- School of Science, Shandong Jiaotong University, Jinan 250357, China; (J.W.); (W.Y.); (L.Z.); (J.Z.)
| | - Juan Zhao
- School of Science, Shandong Jiaotong University, Jinan 250357, China; (J.W.); (W.Y.); (L.Z.); (J.Z.)
| | - Guodong Hu
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
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16
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Nutho B, Tungmunnithum D. Anti-Aging Potential of the Two Major Flavonoids Occurring in Asian Water Lily Using In Vitro and In Silico Molecular Modeling Assessments. Antioxidants (Basel) 2024; 13:601. [PMID: 38790706 PMCID: PMC11118190 DOI: 10.3390/antiox13050601] [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: 04/15/2024] [Revised: 05/11/2024] [Accepted: 05/12/2024] [Indexed: 05/26/2024] Open
Abstract
Our previous study investigated the major flavonoids and antioxidant potential of Asian water lily (Nymphaea lotus L., family Nymphaeaceae) stamens and perianth extracts. Quercetin-3-O-rhamnoside (Que-3-Rha) and kaempferol-3-O-galactoside (Kae-3-Gal) were reported as the two most prominent flavonoids found in these extracts. Many flavonoids have been reported on the skin anti-aging effect that are useful for cosmeceutical/phytopharmaceutical application. However, Que-3-Rha and Kae-3-Gal occurring in this medicinal plant have not yet been evaluated for their ability to inhibit skin-aging enzymes. Therefore, this study aimed (1) to assess the enzyme inhibitory activity of Que-3-Rha and Kae-3-Gal, and (2) to conduct molecular modeling of these compounds against critical enzymes involved in skin aging such as collagenase, elastase, and tyrosinase. In vitro enzymatic assays demonstrated that both of the two most prominent flavonoids exhibited moderate to good inhibitory activity toward these enzymes. These experimental findings were supported by molecular docking analysis, which indicated that Que-3-Rha and Kae-3-Gal showed superior binding affinity to the target enzymes compared to the positive controls. Additionally, computational predictions suggested favorable skin permeability and no severe toxicity for both compounds. The results from molecular dynamic (MD) simulation revealed that all the complexes remained stable during the 200 ns MD simulation. Structural analyses and binding free energy calculations also supported the inhibitory potential of these two flavonoids against skin-aging enzymes. In conclusion, this study provides valuable insights into the anti-aging potential of the two major flavonoids occurring in this medicinal plant, paving the way for further development of cosmeceutical/phytopharmaceutical products targeting skin aging.
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Affiliation(s)
- Bodee Nutho
- Department of Pharmacology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand;
| | - Duangjai Tungmunnithum
- Department of Pharmaceutical Botany, Faculty of Pharmacy, Mahidol University, Bangkok 10400, Thailand
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17
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Kausar N, Shier WT, Ahmed M, Maryam, Albekairi NA, Alshammari A, Saleem M, Imran M, Muddassar M. Investigation of the insecticidal potential of curcumin derivatives that target the Helicoverpa armigera sterol carrier protein-2. Heliyon 2024; 10:e29695. [PMID: 38660259 PMCID: PMC11040122 DOI: 10.1016/j.heliyon.2024.e29695] [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: 09/06/2023] [Revised: 04/12/2024] [Accepted: 04/12/2024] [Indexed: 04/26/2024] Open
Abstract
Cotton bollworm (Helicoverpa armigera) is a highly polyphagous, widely prevalent, and persistent Old World insect pest that affects numerous important crops that are directly consumed by people, including tomato, cotton, pigeon pea, chickpea, rice, sorghum, and cowpea. Insects do not synthesize steroids but obtain them from their diet. Inhibition of dietary uptake of steroids by insects is a potentially effective insecticidal mechanism that should not be toxic to humans and other mammals, who synthesize their steroids. Ten curcumin derivatives were tested against H. armigera sterol carrier protein-2 (HaSCP-2) for their potential as insecticidal agents. Curcumin derivatives were initially docked at the binding site of HaSCP-2 to determine their binding affinities and plausible binding modes. The binding modes predominantly show hydrophobic interactions of derivatives with Phe53, Phe110, and Phe89 as core interacting residues in the active site. Validation of in silico results was carried out by performing a fluorescence binding and displacement assay to determine the binding affinities of curcumin derivatives. Among a collection of curcumin derivatives tested, Cur10 showed the lowest IC50 value of 9.64 μM, while Cur07 was 19.86 μM, and Cur06 was 20.79 μM. There was a significant negative correlation between the ability of the curcumin derivatives tested to displace the fluorescent probe from the sterol binding site of HaSCP-2 and to inhibit Sf9 insect cell growth in culture, which is consistent with the curcumin derivatives acting by the novel mechanism of blocking sterol uptake. Then molecular dynamics simulation studies validated the predicted binding modes and the interactions of curcumin derivatives with HaSCP-2 protein. In conclusion, these studies support the potential use of curcumin derivatives as insecticidal agents.
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Affiliation(s)
- Naeema Kausar
- Department of Biosciences, COMSATS University Islamabad, Park Road, Islamabad, 45550, Pakistan
| | - Wayne Thomas Shier
- College of Pharmacy, Department of Medicinal Chemistry, University of Minnesota, 55455, USA
| | - Mahmood Ahmed
- Department of Chemistry, Division of Science and Technology, University of Education, College Road, Lahore, Pakistan
| | - Maryam
- Department of Biosciences, COMSATS University Islamabad, Park Road, Islamabad, 45550, Pakistan
| | - Norah A. Albekairi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Abdulrahman Alshammari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Muhammad Saleem
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | - Muhammad Imran
- KAM-School of Life Sciences, FC College (A Chartered University), Lahore, 54000, Pakistan
| | - Muhammad Muddassar
- Department of Biosciences, COMSATS University Islamabad, Park Road, Islamabad, 45550, Pakistan
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18
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Sun Q, Chu Y, Zhang N, Chen R, Wang L, Wu J, Dong Y, Li H, Wang L, Tang L, Zhan C, Zhang JQ. Design, Synthesis, Formulation, and Bioevaluation of Trisubstituted Triazines as Highly Selective mTOR Inhibitors for the Treatment of Human Breast Cancer. J Med Chem 2024. [PMID: 38661655 DOI: 10.1021/acs.jmedchem.4c00173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
The aberrant activation of the PI3K/mTOR signaling pathway is implicated in various human cancers. Thus, the development of inhibitors targeting mTOR has attracted considerable attention. In this study, we used a structure-based drug design strategy to discover a highly potent and kinase-selective mTOR inhibitor 24 (PT-88), which demonstrated an mTOR inhibitory IC50 value of 1.2 nM without obvious inhibition against another 195 kinases from the kinase profiling screening. PT-88 displayed selective inhibition against MCF-7 cells (IC50: 0.74 μM) with high biosafety against normal cells, in which autophagy induced by mTOR inhibition was implicated. After successful encapsulation in a lipodisc formulation, PT-88 demonstrated favorable pharmacokinetic and biosafety profiles and exerted a large antitumor effect in an MCF-7 subcutaneous bearing nude mice model. Our study shows the discovery of a highly selective mTOR inhibitor using a structure-based drug discovery strategy and provides a promising antitumor candidate for future study and development.
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Affiliation(s)
- Qiwen Sun
- Guizhou Provincial Engineering Technology Research Center for Chemical Drug R&D, College of Pharmacy, Guizhou Medical University, Guiyang 561113, P. R. China
| | - Yuxiu Chu
- Department of Pharmacy, Shanghai Pudong Hospital & Department of Pharmacology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, P. R. China
| | - Nana Zhang
- Guizhou Provincial Engineering Technology Research Center for Chemical Drug R&D, College of Pharmacy, Guizhou Medical University, Guiyang 561113, P. R. China
| | - Rui Chen
- Guizhou Provincial Engineering Technology Research Center for Chemical Drug R&D, College of Pharmacy, Guizhou Medical University, Guiyang 561113, P. R. China
| | - Lili Wang
- Guizhou Provincial Engineering Technology Research Center for Chemical Drug R&D, College of Pharmacy, Guizhou Medical University, Guiyang 561113, P. R. China
| | - Jiangxia Wu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
| | - Yongxi Dong
- Guizhou Provincial Engineering Technology Research Center for Chemical Drug R&D, College of Pharmacy, Guizhou Medical University, Guiyang 561113, P. R. China
| | - Hongliang Li
- School of Medicine, Yunnan University, 2 Cuihu North Road, Kunming 650091, China
| | - Ling Wang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
| | - Lei Tang
- Guizhou Provincial Engineering Technology Research Center for Chemical Drug R&D, College of Pharmacy, Guizhou Medical University, Guiyang 561113, P. R. China
| | - Changyou Zhan
- Department of Pharmacy, Shanghai Pudong Hospital & Department of Pharmacology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, P. R. China
| | - Ji-Quan Zhang
- Guizhou Provincial Engineering Technology Research Center for Chemical Drug R&D, College of Pharmacy, Guizhou Medical University, Guiyang 561113, P. R. China
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Wang J, Yang W, Zhao L, Wei B, Chen J. Binding Mechanism of Inhibitors to BRD4 and BRD9 Decoded by Multiple Independent Molecular Dynamics Simulations and Deep Learning. Molecules 2024; 29:1857. [PMID: 38675678 PMCID: PMC11054187 DOI: 10.3390/molecules29081857] [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: 04/03/2024] [Revised: 04/16/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
Bromodomain 4 and 9 (BRD4 and BRD9) have been regarded as important targets of drug designs in regard to the treatment of multiple diseases. In our current study, molecular dynamics (MD) simulations, deep learning (DL) and binding free energy calculations are integrated to probe the binding modes of three inhibitors (H1B, JQ1 and TVU) to BRD4 and BRD9. The MD trajectory-based DL successfully identify significant functional function domains, such as BC-loop and ZA-loop. The information from the post-processing analysis of MD simulations indicates that inhibitor binding highly influences the structural flexibility and dynamic behavior of BRD4 and BRD9. The results of the MM-GBSA calculations not only suggest that the binding ability of H1B, JQ1 and TVU to BRD9 are stronger than to BRD4, but they also verify that van der Walls interactions are the primary forces responsible for inhibitor binding. The hot spots of BRD4 and BRD9 revealed by residue-based free energy estimation provide target sites of drug design in regard to BRD4 and BRD9. This work is anticipated to provide useful theoretical aids for the development of selective inhibitors over BRD family members.
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Affiliation(s)
- Jian Wang
- School of Science, Shandong Jiaotong University, Jinan 250357, China
| | - Wanchun Yang
- School of Science, Shandong Jiaotong University, Jinan 250357, China
| | - Lu Zhao
- School of Science, Shandong Jiaotong University, Jinan 250357, China
| | - Benzheng Wei
- Center for Medical Artificial Intelligence, Shandong University of Traditional Chinese Medicine, Qingdao 266112, China
| | - Jianzhong Chen
- School of Science, Shandong Jiaotong University, Jinan 250357, China
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20
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Sun Y, Chen L, Zhao B, Wang R. Molecular docking and molecular dynamics simulation decoding molecular mechanism of EDCs binding to hERRγ. J Mol Model 2024; 30:127. [PMID: 38594491 DOI: 10.1007/s00894-024-05926-z] [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: 10/17/2023] [Accepted: 04/03/2024] [Indexed: 04/11/2024]
Abstract
CONTEXT Human estrogen-related receptor γ (hERRγ) is a key protein involved in various endocrines and metabolic signaling. Numerous environmental endocrine-disrupting chemicals (EDCs) can impact related physiological activities through receptor signaling pathways. Focused on hERRγ with 4-isopropylphenol, bisphenol-F (BPF), and BP(2,2)(Un) complexes, we executed molecular docking and multiple molecular dynamics (MD) simulations along with molecular mechanics/Poisson-Boltzmann surface area (MM-PBSA) and solvation interaction energy (SIE) calculation to study the detailed dynamical structural characteristics and interactions between them. Molecular docking showed that hydrogen bonds and hydrophobic interactions were the prime interactions to keep the stability of BPF-hERRγ and hERRγ-BP(2,2)(Un) complexes. Through MD simulations, we observed that all complexes reach equilibrium during the initial 50 ns of simulation, but these three EDCs lead to local structure changes in hERRγ. Energy results further identified key residues L268, V313, L345, and F435 around the binding pockets through CH-π, π-π, and hydrogen bonds interactions play an important stabilizing role in the recognition with EDCs. And most noticeable of all, hydrophobic methoxide groups in BP(2,2)(Un) is useful for decreasing the binding ability between EDCs and hERRγ. These results may contribute to evaluate latent diseases associated with EDCs exposure at the micro level and find potential substitutes. METHOD Autodock4.2 was used to conduct the molecular docking, sietraj program was performed to calculate the energy, and VMD software was used to visualize the structure. Amber18 was conducted to perform the MD simulation and other analyses.
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Affiliation(s)
- Ying Sun
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar, 161006, China
| | - Lin Chen
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar, 161006, China.
| | - Bing Zhao
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar, 161006, China
- Heilongjiang Provincial Key Laboratory of Surface Active Agent and Auxiliary, Qiqihar University, Qiqihar, 161006, China
| | - Ruige Wang
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar, 161006, China.
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21
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Wang M, Liu K. Molecular dynamics simulations to explore the binding mode between the amyloid-β protein precursor (APP) and adaptor protein Mint2. Sci Rep 2024; 14:7975. [PMID: 38575686 PMCID: PMC10995209 DOI: 10.1038/s41598-024-58584-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 04/01/2024] [Indexed: 04/06/2024] Open
Abstract
Alzheimer's disease (AD) presents a significant challenge in neurodegenerative disease management, with limited therapeutic options available for its prevention and treatment. At the heart of AD pathogenesis is the amyloid-β (Aβ) protein precursor (APP), with the interaction between APP and the adaptor protein Mint2 being crucial. Despite previous explorations into the APP-Mint2 interaction, the dynamic regulatory mechanisms by which Mint2 modulates APP binding remain poorly understood. This study undertakes molecular dynamics simulations across four distinct systems-free Mint2, Mint2 bound to APP, a mutant form of Mint2, and the mutant form bound to APP-over an extensive 400 ns timeframe. Our findings reveal that the mutant Mint2 experiences significant secondary structural transformations, notably the formation of an α-helix in residues S55-K65 upon APP binding, within the 400 ns simulation period. Additionally, we observed a reduction in the active pocket size of the mutant Mint2 compared to its wild-type counterpart, enhancing its APP binding affinity. These insights hold promise for guiding the development of novel inhibitors targeting the Mints family, potentially paving the way for new therapeutic strategies in AD prevention and treatment.
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Affiliation(s)
- Min Wang
- International Research Centre for Nano Handling and Manufacturing of China, Changchun University of Science and Technology, Changchun, 130022, China.
- Ministry of Education Key Laboratory for Cross-Scale Micro and Nano Manufacturing, Changchun University of Science and Technology, Changchun, 130022, China.
| | - Kaifeng Liu
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun, 130012, China
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22
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Xu X, Luo S, Zhao X, Tang B, Zhang E, Liu J, Duan L. Computational analysis of PD-L1 dimerization mechanism induced by small molecules and potential dynamical properties. Int J Biol Macromol 2024; 265:130921. [PMID: 38492688 DOI: 10.1016/j.ijbiomac.2024.130921] [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: 03/13/2024] [Accepted: 03/14/2024] [Indexed: 03/18/2024]
Abstract
The design of small molecule inhibitors that target the programmed death ligand-1 (PD-L1) is a forefront issue in immune checkpoint blocking therapy. Small-molecule inhibitors have been shown to exert therapeutic effects by inducing dimerization of the PD-L1 protein, however, the specific mechanisms underlying this dimerization process remain largely unexplored. Furthermore, there is a notable lack of comparative studies examining the binding modes of structurally diverse inhibitors. In view of the research gaps, this work employed molecular dynamics simulations to meticulously examine the interactions between two distinct types of inhibitors and PD-L1 in both monomeric and dimeric forms, and predicted the dimerization mechanism. The results revealed that inhibitors initially bind to a PD-L1 monomer, subsequently attracting another monomer to form a dimer. Notably, symmetric inhibitors observed superior binding efficiency compared to other inhibitors. Key residues, including Ile54, Tyr56, Met115 and Tyr123 played a leading role in binding. Structurally, symmetric inhibitors were capable of thoroughly engaging the binding pocket, promoting a more symmetrical formation of PD-L1 dimers. Furthermore, symmetric inhibitors formed more extensive hydrophobic interactions with protein residues. The insights garnered from this research are expected to significantly contribute to the rational design and optimization of small molecule inhibitors targeting PD-L1.
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Affiliation(s)
- Xiaole Xu
- School of Physics and Electronics, Shandong Normal University, Jinan 250014, China
| | - Song Luo
- School of Physics and Electronics, Shandong Normal University, Jinan 250014, China
| | - Xiaoyu Zhao
- School of Physics and Electronics, Shandong Normal University, Jinan 250014, China
| | - Bolin Tang
- School of Physics and Electronics, Shandong Normal University, Jinan 250014, China
| | - Enhao Zhang
- School of Physics and Electronics, Shandong Normal University, Jinan 250014, China
| | - Jinxin Liu
- School of Physics and Electronics, Shandong Normal University, Jinan 250014, China
| | - Lili Duan
- School of Physics and Electronics, Shandong Normal University, Jinan 250014, China.
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23
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Jiang D, Du H, Zhao H, Deng Y, Wu Z, Wang J, Zeng Y, Zhang H, Wang X, Wang E, Hou T, Hsieh CY. Assessing the performance of MM/PBSA and MM/GBSA methods. 10. Prediction reliability of binding affinities and binding poses for RNA-ligand complexes. Phys Chem Chem Phys 2024; 26:10323-10335. [PMID: 38501198 DOI: 10.1039/d3cp04366e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
Ribonucleic acid (RNA)-ligand interactions play a pivotal role in a wide spectrum of biological processes, ranging from protein biosynthesis to cellular reproduction. This recognition has prompted the broader acceptance of RNA as a viable candidate for drug targets. Delving into the atomic-scale understanding of RNA-ligand interactions holds paramount importance in unraveling intricate molecular mechanisms and further contributing to RNA-based drug discovery. Computational approaches, particularly molecular docking, offer an efficient way of predicting the interactions between RNA and small molecules. However, the accuracy and reliability of these predictions heavily depend on the performance of scoring functions (SFs). In contrast to the majority of SFs used in RNA-ligand docking, the end-point binding free energy calculation methods, such as molecular mechanics/generalized Born surface area (MM/GBSA) and molecular mechanics/Poisson Boltzmann surface area (MM/PBSA), stand as theoretically more rigorous approaches. Yet, the evaluation of their effectiveness in predicting both binding affinities and binding poses within RNA-ligand systems remains unexplored. This study first reported the performance of MM/PBSA and MM/GBSA with diverse solvation models, interior dielectric constants (εin) and force fields in the context of binding affinity prediction for 29 RNA-ligand complexes. MM/GBSA is based on short (5 ns) molecular dynamics (MD) simulations in an explicit solvent with the YIL force field; the GBGBn2 model with higher interior dielectric constant (εin = 12, 16 or 20) yields the best correlation (Rp = -0.513), which outperforms the best correlation (Rp = -0.317, rDock) offered by various docking programs. Then, the efficacy of MM/GBSA in identifying the near-native binding poses from the decoys was assessed based on 56 RNA-ligand complexes. However, it is evident that MM/GBSA has limitations in accurately predicting binding poses for RNA-ligand systems, particularly compared with notably proficient docking programs like rDock and PLANTS. The best top-1 success rate achieved by MM/GBSA rescoring is 39.3%, which falls below the best results given by docking programs (50%, PLNATS). This study represents the first evaluation of MM/PBSA and MM/GBSA for RNA-ligand systems and is expected to provide valuable insights into their successful application to RNA targets.
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Affiliation(s)
- Dejun Jiang
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China.
- Hangzhou Carbonsilicon AI Technology Co., Ltd, Hangzhou, Zhejiang 310018, China
| | - Hongyan Du
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China.
| | - Huifeng Zhao
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China.
- Hangzhou Carbonsilicon AI Technology Co., Ltd, Hangzhou, Zhejiang 310018, China
| | - Yafeng Deng
- Hangzhou Carbonsilicon AI Technology Co., Ltd, Hangzhou, Zhejiang 310018, China
| | - Zhenxing Wu
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China.
| | - Jike Wang
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China.
| | - Yundian Zeng
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China.
| | - Haotian Zhang
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China.
| | - Xiaorui Wang
- China State Key Laboratory of Quality Research in Chinese Medicines, Macau University of Science and Technology, Macau 999078, China
| | - Ercheng Wang
- Zhejiang Laboratory, Hangzhou, Zhejiang 311100, China.
| | - Tingjun Hou
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China.
| | - Chang-Yu Hsieh
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China.
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24
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Shen C, Yin J, Wang M, Yu Z, Xu X, Zhou Z, Hu Y, Xia C, Hu G. Mutations influence the conformational dynamics of the GDP/KRAS complex. J Biomol Struct Dyn 2024:1-14. [PMID: 38529923 DOI: 10.1080/07391102.2024.2331627] [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: 01/22/2024] [Accepted: 02/20/2024] [Indexed: 03/27/2024]
Abstract
Mutations near allosteric sites can have a significant impact on the function of KRAS. Three specific mutations, K104Q, G12D/K104Q, and G12D/G75A, which are located near allosteric positions, were selected to investigate the molecular mechanisms behind mutation-induced influences on the activity of KRAS. Gaussian accelerated molecular dynamics (GaMD) simulations followed by the principal component analysis (PCA) were performed to improve the sampling of conformational states. The results revealed that these mutations significantly alter the structural flexibility, correlated motions, and dynamic behavior of the switch regions that are essential for KRAS binding to effectors or regulators. Furthermore, the mutations have a significant impact on the hydrogen bonding interactions between GDP and the switch regions, as well as on the electrostatic interactions of magnesium ions (Mg2+) with these regions. Our results verified that these mutations strongly influence the binding of KRAS to its effectors or regulators and allosterically regulate the activity. We believe that this work can provide valuable theoretical insights into a deeper understanding of KRAS function.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Congcong Shen
- Shandong Key Laboratory of Biophysics, Dezhou University, Dezhou, China
| | - Jie Yin
- Qingyun People's Hospital, Dezhou, China
| | - Min Wang
- Qingyun People's Hospital, Dezhou, China
| | - Zhiping Yu
- Shandong Key Laboratory of Biophysics, Dezhou University, Dezhou, China
| | - Xin Xu
- School of Science, Xi'an Polytechnic University, Xi'an, China
| | - Zhongshun Zhou
- School of Science, Xi'an Polytechnic University, Xi'an, China
| | - Yingshi Hu
- Shandong Key Laboratory of Biophysics, Dezhou University, Dezhou, China
| | - Caijuan Xia
- School of Science, Xi'an Polytechnic University, Xi'an, China
| | - Guodong Hu
- Shandong Key Laboratory of Biophysics, Dezhou University, Dezhou, China
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25
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Karnchanapandh K, Sanachai K, Poo-Arporn RP, Rungrotmongkol T. Enhancing bezlotoxumab binding to C. difficile toxin B2: insights from computational simulations and mutational analyses for antibody design. J Biomol Struct Dyn 2024:1-11. [PMID: 38511411 DOI: 10.1080/07391102.2024.2329785] [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: 11/09/2023] [Accepted: 03/06/2024] [Indexed: 03/22/2024]
Abstract
Clostridioides difficile infection (CDI) is a significant concern caused by widespread antibiotic use, resulting in diarrhea and inflammation from the gram-positive anaerobic bacterium C. difficile. Although bezlotoxumab (Bez), a monoclonal antibody (mAb), was developed to address CDI recurrences, the recurrence rate remains high, partly due to reduced neutralization efficiency against toxin B2. In this study, we aimed to enhance the binding of Bez to C. difficile toxin B2 by combining computational simulations and mutational analyses. We identified specific mutations in Bez, including S28R, S31W/K, Y32R, S56W and G103D/S in the heavy chain (Hc), and S32F/H/R/W/Y in the light chain (Lc), which significantly improved binding to toxin B2 and formed critical protein-protein interactions. Through molecular dynamics simulations, several single mutations, such as HcS28R, LcS32H, LcS32R, LcS32W and LcS32Y, exhibited superior binding affinities to toxin B2 compared to Bez wild-type (WT), primarily attributed to Coulombic interactions. Combining the HcS28R mutation with four different mutations at residue LcS32 led to even greater binding affinities in double mutants (MTs), particularly HcS28R/LcS32H, HcS28R/LcS32R and HcS28R/LcS32Y, reinforcing protein-protein binding. Analysis of per-residue decomposition free energy highlighted key residues contributing significantly to enhanced binding interactions, emphasizing the role of electrostatic interactions. These findings offer insights into rational Bez MT design for improved toxin B2 binding, providing a foundation for developing more effective antibodies to neutralize toxin B2 and combat-related infections.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Kun Karnchanapandh
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, Thailand
| | - Kamonpan Sanachai
- Department of Biochemistry, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand
| | - Rungtiva P Poo-Arporn
- Biological Engineering Program, Faculty of Engineering, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Thanyada Rungrotmongkol
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, Thailand
- Center of Excellence in Biocatalyst and Sustainable Biotechnology, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
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26
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de Albuquerque KCO, da Veiga ADSS, Silveira FT, Campos MB, da Costa APL, Brito AKM, Melo PRDS, Percario S, de Molfetta FA, Dolabela MF. Anti-leishmanial activity of Eleutherine plicata Herb. and predictions of isoeleutherin and its analogues. Front Chem 2024; 12:1341172. [PMID: 38510811 PMCID: PMC10950963 DOI: 10.3389/fchem.2024.1341172] [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: 11/19/2023] [Accepted: 02/16/2024] [Indexed: 03/22/2024] Open
Abstract
Introduction: Leishmaniasis is caused by protozoa of the genus Leishmania, classified as tegumentary and visceral. The disease treatment is still a serious problem, due to the toxic effects of available drugs, the costly treatment and reports of parasitic resistance, making the search for therapeutic alternatives urgent. This study assessed the in vitro anti-leishmanial potential of the extract, fractions, and isoeleutherin from Eleutherine plicata, as well as the in silico interactions of isoeleutherin and its analogs with Trypanothione Reductase (TR), in addition to predicting pharmacokinetic parameters. Methods: From the ethanolic extract of E. plicata (EEEp) the dichloromethane fraction (FDEp) was obtained, and isoeleutherin isolated. All samples were tested against promastigotes, and parasite viability was evaluated. Isoeleutherin analogues were selected based on similarity in databases (ZINK and eMolecules) to verify the impact on structural change. Results and Discussion: The extract and its fractions were not active against the promastigote form (IC50 > 200 μg/mL), while isoeleutherin was active (IC50 = 25 μg/mL). All analogues have high intestinal absorption (HIA), cell permeability was moderate in Caco2 and low to moderate in MDCK. Structural changes interfered with plasma protein binding and blood-brain barrier permeability. Regarding metabolism, all molecules appear to be CYP3A4 metabolized and inhibited 2-3 CYPs. Molecular docking and molecular dynamics assessed the interactions between the most stable configurations of isoeleutherin, analogue compound 17, and quinacrine (control drug). Molecular dynamics simulations demonstrated stability and favorable interactions with TR. In summary, fractionation contributed to antileishmanial activity and isoleutherin seems to be promising. Structural alterations did not contribute to improve pharmacokinetic aspects and analogue 17 proved to be more promising than isoeleutherin, presenting better stabilization in TR.
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Affiliation(s)
| | | | | | | | - Ana Paula Lima da Costa
- Laboratory of Molecular Modeling, Institute of Exact and Natural Sciences, Federal University of Pará, Belém, PA, Brazil
| | | | | | - Sandro Percario
- Biotechnology and Biodiversity Postgraduate Program (BIONORTE), Federal University of Pará, Belém, PA, Brazil
| | - Fábio Alberto de Molfetta
- Laboratory of Molecular Modeling, Institute of Exact and Natural Sciences, Federal University of Pará, Belém, PA, Brazil
| | - Maria Fâni Dolabela
- Biotechnology and Biodiversity Postgraduate Program (BIONORTE), Federal University of Pará, Belém, PA, Brazil
- Pharmaceutical Innovation Postgraduate Program, Federal University of Pará, Belém, PA, Brazil
- Faculty of Pharmacy, Federal University of Pará, Belém, PA, Brazil
- Pharmaceutical Sciences Postgraduate Program, Federal University of Pará, Belém, PA, Brazil
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27
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Dawson JRD, Wadman GM, Zhang P, Tebben A, Carter PH, Gu S, Shroka T, Borrega-Roman L, Salanga CL, Handel TM, Kufareva I. Molecular determinants of antagonist interactions with chemokine receptors CCR2 and CCR5. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.15.567150. [PMID: 38014122 PMCID: PMC10680698 DOI: 10.1101/2023.11.15.567150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
By driving monocyte chemotaxis, the chemokine receptor CCR2 shapes inflammatory responses and the formation of tumor microenvironments. This makes it a promising target in inflammation and immuno-oncology; however, despite extensive efforts, there are no FDA-approved CCR2-targeting therapeutics. Cited challenges include the redundancy of the chemokine system, suboptimal properties of compound candidates, and species differences that confound the translation of results from animals to humans. Structure-based drug design can rationalize and accelerate the discovery and optimization of CCR2 antagonists to address these challenges. The prerequisites for such efforts include an atomic-level understanding of the molecular determinants of action of existing antagonists. In this study, using molecular docking and artificial-intelligence-powered compound library screening, we uncover the structural principles of small molecule antagonism and selectivity towards CCR2 and its sister receptor CCR5. CCR2 orthosteric inhibitors are shown to universally occupy an inactive-state-specific tunnel between receptor helices 1 and 7; we also discover an unexpected role for an extra-helical groove accessible through this tunnel, suggesting its potential as a new targetable interface for CCR2 and CCR5 modulation. By contrast, only shape complementarity and limited helix 8 hydrogen bonding govern the binding of various chemotypes of allosteric antagonists. CCR2 residues S1012.63 and V2446.36 are implicated as determinants of CCR2/CCR5 and human/mouse orthosteric and allosteric antagonist selectivity, respectively, and the role of S1012.63 is corroborated through experimental gain-of-function mutagenesis. We establish a critical role of induced fit in antagonist recognition, reveal strong chemotype selectivity of existing structures, and demonstrate the high predictive potential of a new deep-learning-based compound scoring function. Finally, this study expands the available CCR2 structural landscape with computationally generated chemotype-specific models well-suited for structure-based antagonist design.
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Affiliation(s)
- John R D Dawson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Grant M Wadman
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | | | | | - Percy H Carter
- Bristol Myers Squibb Company, Princeton, NJ, USA
- (current affiliation) Blueprint Medicines, Cambridge, MA, USA
| | - Siyi Gu
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- (current affiliation) Lycia Therapeutics, South San Francisco, CA
| | - Thomas Shroka
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- (current affiliation) Avidity Biosciences Inc., San Diego, CA
| | - Leire Borrega-Roman
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Catherina L Salanga
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Tracy M Handel
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Irina Kufareva
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
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28
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Ferreiro D, Khalil R, Sousa SF, Arenas M. Substitution Models of Protein Evolution with Selection on Enzymatic Activity. Mol Biol Evol 2024; 41:msae026. [PMID: 38314876 PMCID: PMC10873502 DOI: 10.1093/molbev/msae026] [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: 09/29/2023] [Revised: 01/25/2024] [Accepted: 01/31/2024] [Indexed: 02/07/2024] Open
Abstract
Substitution models of evolution are necessary for diverse evolutionary analyses including phylogenetic tree and ancestral sequence reconstructions. At the protein level, empirical substitution models are traditionally used due to their simplicity, but they ignore the variability of substitution patterns among protein sites. Next, in order to improve the realism of the modeling of protein evolution, a series of structurally constrained substitution models were presented, but still they usually ignore constraints on the protein activity. Here, we present a substitution model of protein evolution with selection on both protein structure and enzymatic activity, and that can be applied to phylogenetics. In particular, the model considers the binding affinity of the enzyme-substrate complex as well as structural constraints that include the flexibility of structural flaps, hydrogen bonds, amino acids backbone radius of gyration, and solvent-accessible surface area that are quantified through molecular dynamics simulations. We applied the model to the HIV-1 protease and evaluated it by phylogenetic likelihood in comparison with the best-fitting empirical substitution model and a structurally constrained substitution model that ignores the enzymatic activity. We found that accounting for selection on the protein activity improves the fitting of the modeled functional regions with the real observations, especially in data with high molecular identity, which recommends considering constraints on the protein activity in the development of substitution models of evolution.
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Affiliation(s)
- David Ferreiro
- CINBIO, Universidade de Vigo, 36310 Vigo, Spain
- Department of Biochemistry, Genetics and Immunology, Universidade de Vigo, 36310 Vigo, Spain
| | - Ruqaiya Khalil
- CINBIO, Universidade de Vigo, 36310 Vigo, Spain
- Department of Biochemistry, Genetics and Immunology, Universidade de Vigo, 36310 Vigo, Spain
| | - Sergio F Sousa
- UCIBIO/REQUIMTE, BioSIM, Departamento de Biomedicina, Faculdade de Medicina da Universidade do Porto, 4200-319 Porto, Portugal
| | - Miguel Arenas
- CINBIO, Universidade de Vigo, 36310 Vigo, Spain
- Department of Biochemistry, Genetics and Immunology, Universidade de Vigo, 36310 Vigo, Spain
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29
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Karnchanapandh K, Hanpaibool C, Sanachai K, Rungrotmongkol T. Elucidation of bezlotoxumab binding specificity to toxin B in Clostridioides difficile. J Biomol Struct Dyn 2024; 42:1617-1628. [PMID: 37098802 DOI: 10.1080/07391102.2023.2201360] [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: 12/26/2022] [Accepted: 04/05/2023] [Indexed: 04/27/2023]
Abstract
C. difficile or Clostridioides difficile infection (CDI) is currently one of the major causes of epidemics worldwide. Toxin B from Clostridioides difficile toxin B (TcdB) infection is the main target protein inhibiting CDI recurrence. Clinical research suggested that bezlotoxumab's (Bez) efficiency is significantly reduced in neutralizing the B2 strain compared to the B1 strain. The monoclonal antibody (mAb) functions by binding to the epitope 1 and 2 regions in the combined repetitive oligopeptide (CROP) domain. Some binding residues are distinctively different between B1 and B2 strains. In this work, we aimed to elucidate and compare insights into the interaction of toxins B1 and B2 in complex with Bez by using all-atom molecular dynamics (MD) simulations and binding free energy calculations. The predicted ΔGbinding values suggested that the antibody (Ab) could bind to toxin B1 significantly better than B2, supported by higher salt bridge and hydrogen bonding (H-bonding) interactions, as well as the number of contact residues between the two focused proteins. The toxin B1 residues important for binding with Bez were E1878, T1901, E1902, F1905, N1941, V1946, N2031, T2032, E2033, V2076, V2077, and E2092. The lower susceptibility of Bez towards toxin B2 was primarily due to a change of residue E2033 from glutamate to alanine (A2033) and the loss of E1878 and E1902 contributions, as determined by the intermolecular interaction changes from the dynamic residue interaction network (dRIN) analysis. The obtained data strengthen our understanding of Bez/toxin B binding.
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Affiliation(s)
- Kun Karnchanapandh
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, Thailand
| | - Chonnikan Hanpaibool
- Center of Excellence in Biocatalyst and Sustainable Biotechnology, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Kamonpan Sanachai
- Department of Biochemistry, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand
| | - Thanyada Rungrotmongkol
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, Thailand
- Center of Excellence in Biocatalyst and Sustainable Biotechnology, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
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30
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Yu Z, Wang Z, Cui X, Cao Z, Zhang W, Sun K, Hu G. Conformational States of the GDP- and GTP-Bound HRAS Affected by A59E and K117R: An Exploration from Gaussian Accelerated Molecular Dynamics. Molecules 2024; 29:645. [PMID: 38338389 PMCID: PMC10856033 DOI: 10.3390/molecules29030645] [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: 11/27/2023] [Revised: 01/01/2024] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
The HRAS protein is considered a critical target for drug development in cancers. It is vital for effective drug development to understand the effects of mutations on the binding of GTP and GDP to HRAS. We conducted Gaussian accelerated molecular dynamics (GaMD) simulations and free energy landscape (FEL) calculations to investigate the impacts of two mutations (A59E and K117R) on GTP and GDP binding and the conformational states of the switch domain. Our findings demonstrate that these mutations not only modify the flexibility of the switch domains, but also affect the correlated motions of these domains. Furthermore, the mutations significantly disrupt the dynamic behavior of the switch domains, leading to a conformational change in HRAS. Additionally, these mutations significantly impact the switch domain's interactions, including their hydrogen bonding with ligands and electrostatic interactions with magnesium ions. Since the switch domains are crucial for the binding of HRAS to effectors, any alterations in their interactions or conformational states will undoubtedly disrupt the activity of HRAS. This research provides valuable information for the design of drugs targeting HRAS.
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Affiliation(s)
- Zhiping Yu
- Shandong Key Laboratory of Biophysics, Dezhou University, Dezhou 253023, China; (Z.Y.); (Z.C.)
| | - Zhen Wang
- Pingyin People’s Hospital, Jinan 250400, China; (Z.W.); (X.C.)
| | - Xiuzhen Cui
- Pingyin People’s Hospital, Jinan 250400, China; (Z.W.); (X.C.)
| | - Zanxia Cao
- Shandong Key Laboratory of Biophysics, Dezhou University, Dezhou 253023, China; (Z.Y.); (Z.C.)
| | - Wanyunfei Zhang
- School of Science, Xi’an Polytechnic University, Xi’an 710048, China; (W.Z.); (K.S.)
| | - Kunxiao Sun
- School of Science, Xi’an Polytechnic University, Xi’an 710048, China; (W.Z.); (K.S.)
| | - Guodong Hu
- Shandong Key Laboratory of Biophysics, Dezhou University, Dezhou 253023, China; (Z.Y.); (Z.C.)
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31
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Saini S, Kumar Y. Structural and functional analysis of engineered antibodies for cancer immunotherapy: insights into protein compactness and solvent accessibility. J Biomol Struct Dyn 2024:1-14. [PMID: 38173178 DOI: 10.1080/07391102.2023.2300129] [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: 12/22/2023] [Indexed: 01/05/2024]
Abstract
Antibodies are crucial tools in various biomedical applications, including immunotherapy. In this study, we focused on designing and engineering antibodies to enhance their structural dynamics and functional properties. By employing advanced computational techniques and experimental validation, we gained crucial insights into the impact of specific mutations on the engineered antibodies. This study investigates the design and engineering of antibodies to improve their structural dynamics and functional properties. Structural attributes, such as protein compactness and solvent accessibility, were assessed, revealing interesting trends in anti-CD3 and anti-HER2 antibodies. Mutations in CD3 antibodies resulted in a more stable conformation, while mutant HER2 antibodies exhibited altered interaction with the target. Analysis of secondary structure assignments demonstrated significant changes in the folding and stability of the mutant antibodies compared to the wild-type counterparts. The conformational landscape of the engineered antibodies was explored, providing insights into folding pathways and binding mechanisms. Overall, the current study highlights the significance of antibody design and engineering in modulating structural dynamics and functional properties. The findings contribute to developing improved immunotherapeutic strategies by optimising antibody-based therapeutics for targeted diseases with enhanced efficacy and precision.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Samvedna Saini
- Department of Biological Sciences and Engineering (BSE), Netaji Subhas University of Technology (NSUT), New Delhi, India
| | - Yatender Kumar
- Department of Biological Sciences and Engineering (BSE), Netaji Subhas University of Technology (NSUT), New Delhi, India
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32
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He Y, Liu K, Cao F, Song R, Liu J, Zhang Y, Li W, Han W. Using deep learning and molecular dynamics simulations to unravel the regulation mechanism of peptides as noncompetitive inhibitor of xanthine oxidase. Sci Rep 2024; 14:174. [PMID: 38168773 PMCID: PMC10761953 DOI: 10.1038/s41598-023-50686-0] [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: 10/24/2023] [Accepted: 12/22/2023] [Indexed: 01/05/2024] Open
Abstract
Xanthine oxidase (XO) is a crucial enzyme in the development of hyperuricemia and gout. This study focuses on LWM and ALPM, two food-derived inhibitors of XO. We used molecular docking to obtain three systems and then conducted 200 ns molecular dynamics simulations for the Apo, LWM, and ALPM systems. The results reveal a stronger binding affinity of the LWM peptide to XO, potentially due to increased hydrogen bond formation. Notable changes were observed in the XO tunnel upon inhibitor binding, particularly with LWM, which showed a thinner, longer, and more twisted configuration compared to ALPM. The study highlights the importance of residue F914 in the allosteric pathway. Methodologically, we utilized the perturbed response scan (PRS) based on Python, enhancing tools for MD analysis. These findings deepen our understanding of food-derived anti-XO inhibitors and could inform the development of food-based therapeutics for reducing uric acid levels with minimal side effects.
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Affiliation(s)
- Yi He
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Qianjin Road 2699, Changchun, 130012, China
| | - Kaifeng Liu
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Qianjin Road 2699, Changchun, 130012, China
| | - Fuyan Cao
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Qianjin Road 2699, Changchun, 130012, China
| | - Renxiu Song
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Qianjin Road 2699, Changchun, 130012, China
| | - Jianxuan Liu
- Jilin Academy of Chinese Medicine Sciences, Chuangju Road 155, Changchun, 130012, China
| | - Yinghua Zhang
- Jilin Academy of Chinese Medicine Sciences, Chuangju Road 155, Changchun, 130012, China.
| | - Wannan Li
- Edmond H. Fischer Signal Transduction Laboratory, School of Life Sciences, Jilin University, Qianjin Road 2699, Changchun, 130012, China.
| | - Weiwei Han
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Qianjin Road 2699, Changchun, 130012, China.
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Khan MT, Ali A, Wei X, Nadeem T, Muhammad S, Al-Sehemi AG, Wei D. Inhibitory effect of thymoquinone from Nigella sativa against SARS-CoV-2 main protease. An in-silico study. BRAZ J BIOL 2024; 84:e250667. [DOI: 10.1590/1519-6984.25066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Accepted: 01/24/2022] [Indexed: 11/21/2022] Open
Abstract
Abstract Nigella sativa is known for the safety profile, containing a wealth of useful antiviral compounds. The main protease (Mpro, 3CLpro) of severe acute respiratory syndrome 2 (SARS-CoV-2) is being considered as one of the most attractive viral target, processing the polyproteins during viral pathogenesis and replication. In the current investigation we analyzed the potency of active component, thymoquinone (TQ) of Nigella sativa against SARS-CoV-2 Mpro. The structures of TQ and Mpro was retrieved from PubChem (CID10281) and Protein Data Bank (PDB ID 6MO3) respectively. The Mpro and TQ were docked and the complex was subjected to molecular dynamic (MD) simulations for a period 50ns. Protein folding effect was analyzed using radius of gyration (Rg) while stability and flexibility was measured, using root means square deviations (RMSD) and root means square fluctuation (RMSF) respectively. The simulation results shows that TQ is exhibiting good binding activity against SARS-CoV-2 Mpro, interacting many residues, present in the active site (His41, Cys145) and also the Glu166, facilitating the pocket shape. Further, experimental approaches are needed to validate the role of TQ against virus infection. The TQ is interfering with pocket maintaining residues as well as active site of virus Mpro which may be used as a potential inhibitor against SARS-CoV-2 for better management of COVID-19.
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Affiliation(s)
| | - A. Ali
- Shanghai Jiao Tong University, China
| | - X. Wei
- Shanghai Jiao Tong University, China
| | | | | | | | - Dongqing Wei
- Shanghai Jiao Tong University, China; Peng Cheng Laboratory, China
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34
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Patel P, Shrivastava SK, Sharma P, Kurmi BD, Shirbhate E, Rajak H. Hydroxamic acid derivatives as selective HDAC3 inhibitors: computer-aided drug design strategies. J Biomol Struct Dyn 2024; 42:362-383. [PMID: 36995068 DOI: 10.1080/07391102.2023.2192804] [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: 09/01/2022] [Accepted: 03/13/2023] [Indexed: 03/31/2023]
Abstract
Histone deacetylases (HDACs) are critical epigenetic drug targets that have gained significant attention in the scientific community for the treatment of cancer. The currently marketed HDAC inhibitors lack selectivity for the various HDAC isoenzymes. Here, we describe our protocol for the discovery of novel potential hydroxamic acid based HDAC3 inhibitors through pharmacophore modeling, virtual screening, docking, molecular dynamics (MD) simulation and toxicity studies. The ten pharmacophore hypotheses were established, and their reliability was validated by different ROC (receiving operator curve) analysis. Among them, the best model (Hypothesis 9 or RRRA) was employed for searching SCHEMBL, ZINC and MolPort database to screen out hit molecules as selective HDAC3 inhibitors, followed by different docking stages. MD simulation (50 ns) and MMGBSA study were performed to study the stability of ligand binding modes and with the help of trajectory analysis, to calculate the ligand-receptor complex RMSD (root-mean-square deviation), RMSF (root-mean-square fluctuation) and H-bond distance, etc. Finally, in-silico toxicity studies were performed on top screened molecules and compared with reference drug SAHA and established structure-activity relationship (SAR). The results indicated that compound 31, with high inhibitory potency and less toxicity (probability value 0.418), is suitable for further experimental analysis.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Preeti Patel
- Medicinal Chemistry Research Laboratory, Department of Pharmacy, Guru Ghasidas University, Bilaspur, Chhattisgarh, India
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, Moga, Punjab, India
| | - Sushant Kumar Shrivastava
- Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
| | - Piyoosh Sharma
- Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
| | - Balak Das Kurmi
- Department of Pharmaceutics, ISF College of Pharmacy, Moga, Punjab, India
| | - Ekta Shirbhate
- Medicinal Chemistry Research Laboratory, Department of Pharmacy, Guru Ghasidas University, Bilaspur, Chhattisgarh, India
| | - Harish Rajak
- Medicinal Chemistry Research Laboratory, Department of Pharmacy, Guru Ghasidas University, Bilaspur, Chhattisgarh, India
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35
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Chen J, Wang W, Sun H, He W. Roles of Accelerated Molecular Dynamics Simulations in Predictions of Binding Kinetic Parameters. Mini Rev Med Chem 2024; 24:1323-1333. [PMID: 38265367 DOI: 10.2174/0113895575252165231122095555] [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: 03/06/2023] [Revised: 09/05/2023] [Accepted: 10/16/2023] [Indexed: 01/25/2024]
Abstract
Rational predictions on binding kinetics parameters of drugs to targets play significant roles in future drug designs. Full conformational samplings of targets are requisite for accurate predictions of binding kinetic parameters. In this review, we mainly focus on the applications of enhanced sampling technologies in calculations of binding kinetics parameters and residence time of drugs. The methods involved in molecular dynamics simulations are applied to not only probe conformational changes of targets but also reveal calculations of residence time that is significant for drug efficiency. For this review, special attention are paid to accelerated molecular dynamics (aMD) and Gaussian aMD (GaMD) simulations that have been adopted to predict the association or disassociation rate constant. We also expect that this review can provide useful information for future drug design.
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Affiliation(s)
- Jianzhong Chen
- School of Science, Shandong Jiaotong University, Jinan-250357, China
| | - Wei Wang
- School of Science, Shandong Jiaotong University, Jinan-250357, China
| | - Haibo Sun
- School of Science, Shandong Jiaotong University, Jinan-250357, China
| | - Weikai He
- School of Science, Shandong Jiaotong University, Jinan-250357, China
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36
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Sun J, Liang S, Liu X, Zhang S, Li M, Zhang Q, Chen J. Insights into the selectivity of a brain-penetrant CDK4/6 vs CDK1/2 inhibitor for glioblastoma used in multiple replica molecular dynamics simulations. J Biomol Struct Dyn 2023:1-20. [PMID: 38112295 DOI: 10.1080/07391102.2023.2294175] [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: 07/27/2023] [Accepted: 11/23/2023] [Indexed: 12/21/2023]
Abstract
Cyclin dependent kinases (CDKs) play an important role in cell cycle regulation and their dysfunction is associated with many cancers. That is why CDKs have been attractive targets for the treatment of cancer. Glioblastoma is a cancer caused by the aberrant expression of CDK4/6, so exploring the mechanism of the selection of CDK4/6 toward inhibitors relative to the other family members CDK1/2 is essential. In this work, multiple replica molecular dynamics (MRMD) simulations, principal component analysis (PCA), free energy landscapes (FELs), molecular mechanics Poisson-Boltzmann/Generalized Born surface area (MM-PB/GBSA) and other methods were integrated to decipher the selectively binding mechanism of the inhibitor N1J to CDK4/6 and CDK1/2. Molecular electrostatic potential (MESP) analysis provides an explanation for the N1J selectivity. Residue-based free energy decomposition reveals that most of the hot residues are located at the same location of CDKs proteins, but the different types of residues in different proteins cause changes in binding energy, which is considered as a potential developmental direction to improve the selectivity of inhibitors to CDK4/6. These results provide insights into the source of inhibitor and CDK4/6 selectivity for the future development of more selective inhibitors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jiahao Sun
- School of Physics and Electronics, Shandong Normal University, Jinan, China
| | - Shanshan Liang
- School of Physics and Electronics, Shandong Normal University, Jinan, China
| | - Xinguo Liu
- School of Physics and Electronics, Shandong Normal University, Jinan, China
| | - Shaolong Zhang
- School of Physics and Electronics, Shandong Normal University, Jinan, China
| | - Meng Li
- School of Physics and Electronics, Shandong Normal University, Jinan, China
| | - Qinggang Zhang
- School of Physics and Electronics, Shandong Normal University, Jinan, China
| | - Jianzhong Chen
- School of Science, Shandong Jiaotong University, Jinan, China
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37
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Caputa DA, Blankenship QP, Smith ZD, Huebner MM, Vetter ZA, Parks RW, Armendariz Lobera S, Leddin EM, Taylor CA, Parish CA, Miller BR. Computational drug discovery of an inhibitor of APOBEC3B as a treatment for epithelial cancers. J Biomol Struct Dyn 2023:1-14. [PMID: 38109103 DOI: 10.1080/07391102.2023.2293269] [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: 03/09/2023] [Accepted: 11/29/2023] [Indexed: 12/19/2023]
Abstract
Cancer is one of the leading causes of death in the U.S., and tumorous cancers such as cervical, lung, breast, and ovarian cancers are the most common types. APOBEC3B is a nonessential cytidine deaminase found in humans and theorized to defend against viral infection. However, overexpression of APOBEC3B is linked to cancer in humans, which makes APOBEC3B a potential cancer treatment target through competitive inhibition for several tumorous cancers. Computational studies can help reveal a small molecule inhibitor using high-throughput virtual screening of millions of candidates with relatively little cost. This study aims to narrow the field of potential APOBEC3B inhibition candidates for future in vitro assays and provide an effective scaffold for drug design studies. Another goal of this project is to provide critical amino acid targets in the active site for future drug design studies. This study simulated 7.8 million drug candidates using high-throughput virtual screening and further processed the top scoring 241 molecules from AutoDock Vina, DOCK 6, and de novo design. Using virtual screening, de novo design, and molecular dynamics simulations, a competitive inhibitor candidate was discovered with an average binding free energy score of -46.03 kcal/mol, more than 10 kcal/mol better than the substrate control (dCMP). These results indicate that this molecule (or a structural derivative) may be an effective inhibitor of APOBEC3B and prevent host genome mutagenesis resulting from protein overexpression. Another important finding is the confirmation of essential amino acid targets, such as Tyr250 and Gln213 within the active site of APOBEC3B. Therefore, study used novel computational methods to provide a theoretical scaffold for future drug design studies that may prove useful as a treatment for epithelial cancers.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Dominic A Caputa
- Physics Department, Truman State University, Kirksville, MO, USA
| | | | - Zachary D Smith
- Chemistry Department, Truman State University, Kirksville, MO, USA
- Biology Department, Truman State University, Kirksville, MO, USA
| | - Molly M Huebner
- Chemistry Department, Truman State University, Kirksville, MO, USA
| | - Zoe A Vetter
- Physics Department, Truman State University, Kirksville, MO, USA
- Chemistry Department, Truman State University, Kirksville, MO, USA
| | - Richard W Parks
- Chemistry Department, Truman State University, Kirksville, MO, USA
- Biology Department, Truman State University, Kirksville, MO, USA
| | | | - Emmett M Leddin
- Chemistry Department, Truman State University, Kirksville, MO, USA
| | - Cooper A Taylor
- Department of Chemistry, University of Richmond, Richmond, VA, USA
| | - Carol A Parish
- Department of Chemistry, University of Richmond, Richmond, VA, USA
| | - Bill R Miller
- Chemistry Department, Truman State University, Kirksville, MO, USA
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38
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Wanas AS, Radwan MM, Marzouk AA, Elkaeed EB, Alsfouk BA, Mostafa AE, Eissa IH, Metwaly AM, ElSohly MA. Isolation and in silico investigation of cannflavins from Cannabis sativa leaves as potential anti-SARS-CoV-2 agents targeting the Papain-Like Protease. Nat Prod Res 2023:1-14. [PMID: 38100380 DOI: 10.1080/14786419.2023.2294111] [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: 06/15/2023] [Accepted: 12/03/2023] [Indexed: 12/17/2023]
Abstract
This study aimed to isolate and identify three prenylflavonoids (cannflavin A, B, and C) from Cannabis sativa leaves using different chromatographic techniques. The potential of the isolated compounds against SARS-CoV-2 was suggested through several in silico analysis. Structural similarity studies against nine co-crystallized ligands of SARS-CoV-2's proteins indicated the similarities of the isolated cannflavins with the SARS-CoV-2 Papain-Like Protease (PLP) ligand, Y95. Then, flexible allignment study confirmed this similarity. Docking experiments showed successful binding of all cannflavins within the active pocket of PLP, with energies comparable to Y95. Among them, cannflavin A demonstrated the most similar binding mode, while cannflavin C exhibited the best energy. Molecular dynamics (MD) simulations and MM-GPSA confirmed the accurate binding of cannflavin A to the PLP. In silico ADMET studies indicated favourable drug-like properties for all three compounds, suggesting their potential as anti-SARS-CoV-2 agents. Further In vitro and In vivo investigations are necessary to validate these findings and establish their efficacy and safety profiles.
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Affiliation(s)
- Amira S Wanas
- National Center for Natural Products Research, School of Pharmacy, University of Mississippi, University, Mississippi, USA
- Department of Pharmacognosy, Faculty of Pharmacy, Minia University, Minia, Egypt
| | - Mohamed M Radwan
- National Center for Natural Products Research, School of Pharmacy, University of Mississippi, University, Mississippi, USA
| | - Adel A Marzouk
- National Center for Natural Products Research, School of Pharmacy, University of Mississippi, University, Mississippi, USA
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Al-Azhar University, Assiut, Egypt
| | - Eslam B Elkaeed
- Department of Pharmaceutical Sciences, College of Pharmacy, AlMaarefa University, Riyadh, Saudi Arabia
| | - Bshra A Alsfouk
- Department of Pharmaceutical Sciences, College of Pharmacy, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Ahmad E Mostafa
- Pharmacognosy and Medicinal Plants Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo, Egypt
| | - Ibrahim H Eissa
- Pharmaceutical Medicinal Chemistry & Drug Design Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo, Egypt
| | - Ahmed M Metwaly
- Pharmacognosy and Medicinal Plants Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo, Egypt
- Biopharmaceutical Products Research Department, Genetic Engineering and Biotechnology Research Institute, City of Scientific Research and Technological Applications (SRTA-City), Alexandria, Egypt
| | - Mahmoud A ElSohly
- National Center for Natural Products Research, School of Pharmacy, University of Mississippi, University, Mississippi, USA
- Department of Pharmaceutics and Drug Delivery, School of Pharmacy, University, Mississippi, USA
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39
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Zhao TT, Hu HJ, Gao LX, Zhou YB, Zhu YL, Zhang C, Li J, Wang WL. Exploring the mechanism of the PTP1B inhibitors by molecular dynamics and experimental study. J Mol Graph Model 2023; 125:108585. [PMID: 37544021 DOI: 10.1016/j.jmgm.2023.108585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 07/27/2023] [Accepted: 07/31/2023] [Indexed: 08/08/2023]
Abstract
Protein tyrosine phosphatase 1B (PTP1B) has proven to be an attractive target for the treatment of cancer, diabetes and other diseases. Although many PTP1B inhibitors with various scaffolds have been developed, there is still a lack of PTP1B inhibitor with high specificity and acceptable pharmacological properties. Therefore, it is urgent to develop more methods to explore complex action mode of PTP1B and ligands for designing ideal PTP1B modulators. In this work, we developed a potential molecular dynamics (MD) analytic mode to analyze the mechanism of active compounds 6a and 6e against PTP1B from different perspectives, including the stable ability, interactions and binding site of ligand and protein, the binding energy, relative movement between residues and changes in protein internal interactions. The simulated results demonstrated that compound 6a bound more stably to the active pocket of PTP1B than 6e due to its smaller molecular volume (326 Å3), matched electronegativity, and enhanced the positive correlation motion of residues, especially for WPD loop and P loop. Lastly, compound 6a as a competitive inhibitor for PTP1B was verified by enzyme kinetic assay. This work successfully studied the mechanism of compound 6a against PTP1B from various aspects, enriched the analysis of interaction mode between PTP1B and inhibitors. In summary, we hope that this work could provide more theoretical information for designing and developing more novel and ideal PTP1B inhibitors in the future.
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Affiliation(s)
- Tian-Tian Zhao
- School of Life Sciences and Health Engineering, Jiangnan University, Jiangsu, 214122, China
| | - Hao-Jie Hu
- School of Life Sciences and Health Engineering, Jiangnan University, Jiangsu, 214122, China
| | - Li-Xin Gao
- School of Life Sciences and Health Engineering, Jiangnan University, Jiangsu, 214122, China; State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Yu-Bo Zhou
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Yun-Long Zhu
- Wuxi Maternal and Child Health Hospital, Wuxi School of Medicine, Jiangnan University, Jiangsu, 214002, China.
| | - Chun Zhang
- School of Life Sciences and Health Engineering, Jiangnan University, Jiangsu, 214122, China.
| | - Jia Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
| | - Wen-Long Wang
- School of Life Sciences and Health Engineering, Jiangnan University, Jiangsu, 214122, China.
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40
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Irfan A, Faisal S, Ahmad S, Saif MJ, Zahoor AF, Khan SG, Javid J, Al-Hussain SA, Muhammed MT, Zaki MEA. An Exploration of the Inhibitory Mechanism of Rationally Screened Benzofuran-1,3,4-Oxadiazoles and-1,2,4-Triazoles as Inhibitors of NS5B RdRp Hepatitis C Virus through Pharmacoinformatic Approaches. Biomedicines 2023; 11:3085. [PMID: 38002085 PMCID: PMC10669698 DOI: 10.3390/biomedicines11113085] [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: 10/10/2023] [Revised: 11/02/2023] [Accepted: 11/03/2023] [Indexed: 11/26/2023] Open
Abstract
Benzofuran, 1,3,4-oxadiazole, and 1,2,4-triazole are privileged heterocyclic moieties that display the most promising and wide spectrum of biological activities against a wide variety of diseases. In the current study, benzofuran-1,3,4-oxadiazole BF1-BF7 and benzofuran-1,2,4-triazole compounds BF8-BF15 were tested against HCV NS5B RNA-dependent RNA polymerase (RdRp) utilizing structure-based screening via a computer-aided drug design (CADD) approach. A molecular docking approach was applied to evaluate the binding potential of benzofuran-appended 1,3,4-oxadiazole and 1,2,4-triazole BF1-BF15 molecules. Benzofuran-1,3,4-oxadiazole scaffolds BF1-BF7 showed lesser binding affinities (-12.63 to -14.04 Kcal/mol) than benzofuran-1,2,4-triazole scaffolds BF8-BF15 (-14.11 to -16.09 Kcal/mol) against the HCV NS5B enzyme. Molecular docking studies revealed the excellent binding affinity scores exhibited by benzofuran-1,2,4-triazole structural motifs BF-9 (-16.09 Kcal/mol), BF-12 (-15.75 Kcal/mol), and BF-13 (-15.82 Kcal/mol), respectively, which were comparatively better than benzofuran-based HCV NS5B inhibitors' standard reference drug Nesbuvir (-15.42 Kcal/mol). A molecular dynamics simulation assay was also conducted to obtain valuable insights about the enzyme-compounds interaction profile and structural stability, which indicated the strong intermolecular energies of the BF-9+NS5B complex and the BF-12+NS5B complex as per the MM-PBSA method, while the BF-12+NS5B complex was the most stable system as per the MM-GBSA calculation. The drug-likeness and ADMET studies of all the benzofuran-1,2,4-triazole derivatives BF8-BF15 revealed that these compounds possessed good medicinal chemistry profiles in agreement with all the evaluated parameters for being drugs. The molecular docking affinity scores, MM-PBSA/MM-GBSA and MD-simulation stability analysis, drug-likeness profiling, and ADMET study assessment indicated that N-4-fluorophenyl-S-linked benzofuran-1,2,4-triazole BF-12 could be a future promising anti-HCV NS5B RdRp inhibitor therapeutic drug candidate that has a structural agreement with the Nesbuvir standard reference drug.
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Affiliation(s)
- Ali Irfan
- Department of Chemistry, Government College University Faisalabad, Faisalabad 38000, Pakistan; (A.I.); (A.F.Z.)
| | - Shah Faisal
- Department of Chemistry, Islamia College University Peshawar, Peshawar 25120, Pakistan
| | - Sajjad Ahmad
- Department of Health and Biological Sciences, Abasyn University Peshawar, Peshawar 25000, Pakistan
- Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut P.O. Box 36, Lebanon
- Department of Natural Sciences, Lebanese American University, Beirut P.O. Box 36, Lebanon
| | - Muhammad Jawwad Saif
- Department of Applied Chemistry, Government College University Faisalabad, Faisalabad 38000, Pakistan
| | - Ameer Fawad Zahoor
- Department of Chemistry, Government College University Faisalabad, Faisalabad 38000, Pakistan; (A.I.); (A.F.Z.)
| | - Samreen Gul Khan
- Department of Chemistry, Government College University Faisalabad, Faisalabad 38000, Pakistan; (A.I.); (A.F.Z.)
| | - Jamila Javid
- Department of Chemistry, University of Sialkot, Sialkot 51040, Pakistan
| | - Sami A. Al-Hussain
- Department of Chemistry, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 13623, Saudi Arabia
| | - Muhammed Tilahun Muhammed
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Suleyman Demirel University, Isparta 32260, Turkey
| | - Magdi E. A. Zaki
- Department of Chemistry, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 13623, Saudi Arabia
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41
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Zhang NN, Ban YJ, Wang YJ, He SY, Qi PP, Bi T, Ma YF, Dong YX, Guo B, Weng J, Li HL, Tang L, Zhang JQ. Virtual screening of novel mTOR inhibitors for the potential treatment of human colorectal cancer. Bioorg Chem 2023; 140:106781. [PMID: 37597440 DOI: 10.1016/j.bioorg.2023.106781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 08/04/2023] [Accepted: 08/08/2023] [Indexed: 08/21/2023]
Abstract
The abnormal activation of the mTOR pathway is closely related to the occurrence and progression of cancer, especially colorectal cancer. In this study, a rational virtual screening strategy has been established and MT-5, a novel mTOR inhibitor with a quinoline scaffold, was obtained from the ChemDiv database. MT-5 showed potent kinase inhibitory activity (IC50: 8.90 μM) and antiproliferative effects against various cancer cell lines, especially HCT-116 cells (IC50: 4.61 μM), and this was 2.2-fold more potent than that of the cisplatin control (IC50: 9.99 μM). Western blot, cell migration, cycle arrest, and apoptosis assays were performed with HCT-116 cells to investigate the potential anticancer mechanism of MT-5. Metabolic stability results in vitro indicated that MT-5 exhibited good stability profiles in artificial gastrointestinal fluids, rat plasma, and liver microsomes. In addition, the key contribution of the residues around the binding pocket of MT-5 in binding to the mTOR protein was also investigated from a computational perspective.
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Affiliation(s)
- Na-Na Zhang
- Guizhou Provincial Engineering Technology Research Center for Chemical Drug R&D, College of Pharmacy, Guizhou Medical University, Guiyang 550025, China
| | - Yu-Juan Ban
- Guizhou Provincial Engineering Technology Research Center for Chemical Drug R&D, College of Pharmacy, Guizhou Medical University, Guiyang 550025, China
| | - Yu-Jie Wang
- Guizhou Provincial Engineering Technology Research Center for Chemical Drug R&D, College of Pharmacy, Guizhou Medical University, Guiyang 550025, China
| | - Si-Yu He
- Guizhou Provincial Engineering Technology Research Center for Chemical Drug R&D, College of Pharmacy, Guizhou Medical University, Guiyang 550025, China
| | - Pan-Pan Qi
- Guizhou Provincial Engineering Technology Research Center for Chemical Drug R&D, College of Pharmacy, Guizhou Medical University, Guiyang 550025, China
| | - Ting Bi
- The Affiliated Hospital of Guizhou Medical University, Guiyang 550004, China
| | - Yi-Fei Ma
- The Affiliated Hospital of Guizhou Medical University, Guiyang 550004, China
| | - Yong-Xi Dong
- Guizhou Provincial Engineering Technology Research Center for Chemical Drug R&D, College of Pharmacy, Guizhou Medical University, Guiyang 550025, China
| | - Bing Guo
- Guizhou Provincial Key Laboratory of Pathogenesis and Drug Research on Common Chronic Diseases, Guizhou Medical University, Guiyang 550025, China
| | - Jiang Weng
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Hong-Liang Li
- School of Medicine, Yunnan University, 2 Cuihu North Road, Kunming 650091, China
| | - Lei Tang
- Guizhou Provincial Engineering Technology Research Center for Chemical Drug R&D, College of Pharmacy, Guizhou Medical University, Guiyang 550025, China
| | - Ji-Quan Zhang
- Guizhou Provincial Engineering Technology Research Center for Chemical Drug R&D, College of Pharmacy, Guizhou Medical University, Guiyang 550025, China.
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Sun J, Liu X, Zhang S, Li M, Zhang Q, Chen J. Molecular insights and optimization strategies for the competitive binding of engineered ACE2 proteins: a multiple replica molecular dynamics study. Phys Chem Chem Phys 2023; 25:28479-28496. [PMID: 37846774 DOI: 10.1039/d3cp03392a] [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: 10/18/2023]
Abstract
The COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) continues to spread globally, and rapid viral evolution and the emergence of new variants pose challenges to pandemic control. During infection, the spike protein of SARS-CoV-2 interacts with the human ACE2 protein via its receptor binding domain (RBD), and it is known that engineered forms of ACE2 can compete with wild-type (WT) ACE2 for binding to inhibit infection. Here, we conducted multiple replica molecular dynamics (MRMD) simulations to study the mechanisms of the engineered ACE2 variants 3N39 and 3N94 and provide directions for optimization. Our findings reveal that engineered ACE2 is notably more efficacious in systems that show weaker binding to WT ACE2 (i.e., WT and BA.1 RBD), but also faces immune escape as the virus evolves. Moreover, by modifying residue types near the binding interface, engineered ACE2 alters the electrostatic potential distribution and reconfigures the hydrogen bonding network, which results in modified binding to the RBD. However, this structural rearrangement does not occur in all RBD variants. In addition, we identified potentially engineerable beneficial residues and potentially engineerable detrimental residues in both ACE2 and RBD. Functional conservation can thus enable the optimization of these residues and improve the binding competitiveness of engineered ACE2, which therefore provides additional immune escape prevention. Finally, we conclude that these findings have implications for understanding the mechanisms responsible for engineered ACE2 and can help us to develop engineered ACE2 proteins that show superior performance.
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Affiliation(s)
- Jiahao Sun
- School of Physics and Electronics, Shandong Normal University, Jinan, 250358, China.
| | - Xinguo Liu
- School of Physics and Electronics, Shandong Normal University, Jinan, 250358, China.
| | - Shaolong Zhang
- School of Physics and Electronics, Shandong Normal University, Jinan, 250358, China.
| | - Meng Li
- School of Physics and Electronics, Shandong Normal University, Jinan, 250358, China.
| | - Qinggang Zhang
- School of Physics and Electronics, Shandong Normal University, Jinan, 250358, China.
| | - Jianzhong Chen
- School of Science, Shandong Jiaotong University, Jinan, 250357, China.
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Shoaib TH, Almogaddam MA, Andijani YS, Saib SA, Almaghrabi NM, Elyas AF, Azzouni RY, Awad EA, Mohamed SGA, Mohamed GA, Ibrahim SRM, Hussein HGA, Osman W, Ashour A, Sherif AE, Alzain AA. Marine-Derived Compounds for CDK5 Inhibition in Cancer: Integrating Multi-Stage Virtual Screening, MM/GBSA Analysis and Molecular Dynamics Investigations. Metabolites 2023; 13:1090. [PMID: 37887415 PMCID: PMC10608970 DOI: 10.3390/metabo13101090] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 10/07/2023] [Accepted: 10/17/2023] [Indexed: 10/28/2023] Open
Abstract
Cyclin-dependent kinase 5 (CDK5) plays a crucial role in various biological processes, including immune response, insulin secretion regulation, apoptosis, DNA (deoxyribonucleic acid) damage response, epithelial-mesenchymal transition (EMT), cell migration and invasion, angiogenesis, and myogenesis. Overactivation of CDK5 is associated with the initiation and progression of cancer. Inhibiting CDK5 has shown potential in suppressing cancer development. Despite advancements in CDK5-targeted inhibitor research, the range of compounds available for clinical and preclinical trials remains limited. The marine environment has emerged as a prolific source of diverse natural products with noteworthy biological activities, including anti-cancer properties. In this study, we screened a library of 47,450 marine natural compounds from the comprehensive marine natural product database (CMNPD) to assess their binding affinity with CDK5. Marine compounds demonstrating superior binding affinity compared to a reference compound were identified through high-throughput virtual screening, standard precision and extra-precision Glide docking modes. Refinement of the selected molecules involved evaluating molecular mechanics-generalized born surface area (MM/GBSA) free binding energy. The three most promising compounds, (excoecariphenol B, excoecariphenol A, and zyzzyanone B), along with the reference, exhibiting favorable binding characteristics were chosen for molecular dynamics (MD) simulations for 200 nanoseconds. These compounds demonstrated interaction stability with the target during MD simulations. The marine compounds identified in this study hold potential as effective CDK5 inhibitors and warrant subsequent experimental validation.
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Affiliation(s)
- Tagyedeen H. Shoaib
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Wad Madani 21111, Sudan; (T.H.S.); (M.A.A.)
| | - Mohammed A. Almogaddam
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Wad Madani 21111, Sudan; (T.H.S.); (M.A.A.)
| | - Yusra Saleh Andijani
- Department of Pharmacology and Toxicology, College of Pharmacy, Taibah University, Al-Madinah Al-Munawwarah 30078, Saudi Arabia;
| | | | | | - Abdulaziz Fahad Elyas
- Emergency Medical Services Department, Madinah National Hospital, Madinah 11461, Saudi Arabia;
| | - Rahmah Yasin Azzouni
- King Faisal Specialist Hospital & Research Center, Al-Madinah Al-Munawwarah 42523, Saudi Arabia;
| | - Ehda Ahmad Awad
- Prince Mohammed Bin Abdulaziz Hospital-Al Madinah Al Munawarah-NGHA, Ministry of National Guard Health Affairs, Kingdom of Saudi Arabia, Riyadh 41511, Saudi Arabia;
| | - Shaimaa G. A. Mohamed
- Faculty of Dentistry, British University, El Sherouk City, Suez Desert Road, Cairo 11837, Egypt;
| | - Gamal A. Mohamed
- Department of Natural Products and Alternative Medicine, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
| | - Sabrin R. M. Ibrahim
- Preparatory Year Program, Department of Chemistry, Batterjee Medical College, Jeddah 21442, Saudi Arabia
- Department of Pharmacognosy, Faculty of Pharmacy, Assiut University, Assiut 71526, Egypt
| | - Hazem G. A. Hussein
- Preparatory Year Program, Batterjee Medical College, Jeddah 21442, Saudi Arabia;
| | - Wadah Osman
- Department of Pharmacognosy, Faculty of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-kharj 11942, Saudi Arabia; (W.O.); (A.A.); (A.E.S.)
- Department of Pharmacognosy, Faculty of Pharmacy, University of Khartoum, Al-Qasr Ave., Khartoum 11111, Sudan
| | - Ahmed Ashour
- Department of Pharmacognosy, Faculty of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-kharj 11942, Saudi Arabia; (W.O.); (A.A.); (A.E.S.)
- Department of Pharmacognosy, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Asmaa E. Sherif
- Department of Pharmacognosy, Faculty of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-kharj 11942, Saudi Arabia; (W.O.); (A.A.); (A.E.S.)
- Department of Pharmacognosy, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Abdulrahim A. Alzain
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Gezira, Wad Madani 21111, Sudan; (T.H.S.); (M.A.A.)
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Sitthiyotha T, Treewattanawong W, Chunsrivirot S. Designing peptides predicted to bind to the omicron variant better than ACE2 via computational protein design and molecular dynamics. PLoS One 2023; 18:e0292589. [PMID: 37816037 PMCID: PMC10564162 DOI: 10.1371/journal.pone.0292589] [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: 04/25/2023] [Accepted: 09/25/2023] [Indexed: 10/12/2023] Open
Abstract
Brought about by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), coronavirus disease (COVID-19) pandemic has resulted in large numbers of worldwide deaths and cases. Several SARS-CoV-2 variants have evolved, and Omicron (B.1.1.529) was one of the important variants of concern. It gets inside human cells by using its S1 subunit's receptor-binding domain (SARS-CoV-2-RBD) to bind to Angiotensin-converting enzyme 2 receptor's peptidase domain (ACE2-PD). Using peptides to inhibit binding interactions (BIs) between ACE2-PD and SARS-CoV-2-RBD is one of promising COVID-19 therapies. Employing computational protein design (CPD) as well as molecular dynamics (MD), this study used ACE2-PD's α1 helix to generate novel 25-mer peptide binders (SPB25) of Omicron RBD that have predicted binding affinities (ΔGbind (MM‑GBSA)) better than ACE2 by increasing favorable BIs between SPB25 and the conserved residues of RBD. Results from MD and the MM-GBSA method identified two best designed peptides (SPB25T7L/K11A and SPB25T7L/K11L with ΔGbind (MM‑GBSA) of -92.4 ± 0.4 and -95.7 ± 0.5 kcal/mol, respectively) that have better ΔGbind (MM‑GBSA) to Omicron RBD than ACE2 (-87.9 ± 0.5 kcal/mol) and SPB25 (-71.6 ± 0.5 kcal/mol). Additionally, they were predicted to have slightly higher stabilities, based on their percent helicities in water, than SBP1 (the experimentally proven inhibitor of SARS-CoV-2-RBD). Our two best designed SPB25s are promising candidates as omicron variant inhibitors.
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Affiliation(s)
- Thassanai Sitthiyotha
- Structural and Computational Biology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok, Thailand
| | - Wantanee Treewattanawong
- Structural and Computational Biology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok, Thailand
| | - Surasak Chunsrivirot
- Structural and Computational Biology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok, Thailand
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Rehman MU, Ali A, Ansar R, Arafah A, Imtiyaz Z, Wani TA, Zargar S, Ganie SA. In Silico molecular docking and dynamic analysis of natural compounds against major non-structural proteins of SARS-COV-2. J Biomol Struct Dyn 2023; 41:9072-9088. [PMID: 36326281 DOI: 10.1080/07391102.2022.2139766] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 10/19/2022] [Indexed: 11/06/2022]
Abstract
COVID-19 has infected millions and significantly affected the global economy and healthcare systems. Despite continuous lockdowns, symptomatic management with currently available medications, and numerous vaccination drives, it is still far more difficult to control. Against COVID-19 infection, the pressure to develop vaccines and drugs has led to using some currently available medications like remdesivir, azithromycin, hydroxychloroquine and ritonavir. Understanding the importance and potential of harmless molecules to tackle SARS-COV-2, we designed the present study to identify potential natural phytocompounds. In the present study, we docked natural compounds and standard drugs against SARS-COV-2 proteins: papain-like protease, main protease and helicase. ADME/T and ProTox-II analyses were used to determine the toxicity of phytocompounds and drugs. The docking analysis revealed that podophyllotoxin gave the highest binding affinity scores of -8.1, -7.1 and -7.4 kcal/mol against PLpro, Mpro and helicase, respectively. Among the control drugs, doxycycline hydrochloride showed the highest binding affinity of -10.5, -8.4 and -8.8 kcal/mol against PLpro, Mpro and helicase. The results of this study revealed that podophyllotoxin and doxycycline hydrochloride could be promising inhibitors against SARS-Cov-2. Molecular dynamic simulations were executed for the best docked (PLpro-podophyllotoxin) complex, and the results displayed stable conformation and convergence. Energy plot results predicted a global minima average energy of -95 kcal/mol and indicated podophyllotoxin's role in stabilizing protein and making it compact and complex. FarPPI server used MM/GBSA approach to determine free binding affinity, and helicase-gallic acid complex showed the highest affinity, respectively. Therefore, it can be concluded that there is still a need for in vitro and in vivo studies to support further and validate these findings and validate these findings.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Muneeb U Rehman
- Department of Clinical Pharmacy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Aarif Ali
- Department of Clinical Biochemistry, School of Biological Sciences, University of Kashmir, Hazratbal, Srinagar, J&K, India
| | - Ruhban Ansar
- Department of Clinical Biochemistry, School of Biological Sciences, University of Kashmir, Hazratbal, Srinagar, J&K, India
| | - Azher Arafah
- Department of Clinical Pharmacy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Zuha Imtiyaz
- Department of Pathology, University Maryland School of Medicine, University of Maryland, Baltimore, MD, USA
| | - Tanveer A Wani
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Seema Zargar
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Showkat A Ganie
- Department of Clinical Biochemistry, School of Biological Sciences, University of Kashmir, Hazratbal, Srinagar, J&K, India
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Malla BA, Ali A, Maqbool I, Dar NA, Ahmad SB, Alsaffar RM, Rehman MU. Insights into molecular docking and dynamics to reveal therapeutic potential of natural compounds against P53 protein. J Biomol Struct Dyn 2023; 41:8762-8781. [PMID: 36281711 DOI: 10.1080/07391102.2022.2137241] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 10/11/2022] [Indexed: 10/31/2022]
Abstract
P53 is eminent tumour suppressor protein that plays a prominent role in cell cycle arrest, DNA repair, senescence, differentiation and initiation of apoptosis. P53 is an attractive drug target and the high toxicity of some cancer chemotherapy drugs increase the demand for new anti-cancer drugs from natural products. In this current scenario, identification of promising anticancer compounds from natural sources by repurposing approach is still relevant for the early prevention and effective management of cancer. In present study, we docked natural compounds like podophyllotoxin, quercetin and rutin along standard drugs (MG-132 and Bay 61-3606) against p53 protein. ADME/T analysis predicted toxicity of phytochemicals and drugs. In silico docking analysis of podophyllotoxin, quercetin and rutin gave HDOCK docking scores of -187.87, -148. 97 and -143.85, whereas control drugs MG-132 and Bay 61-3606 showed docking scores of -159.59 and -140.71 against p53 respectively. AutoDock analysis of rutin and MG-132 showed highest binding affinity scores of -7.3 and -6.8 kcal/mol against p53. Molecular dynamic simulation for p53 protein displayed stable conformation and convergence. In this study, P53-rutin complex showed free binding energy score of 11.84 kcal/mol and P53-MG-132 complex reported free energy score of 16.3 kcal/mol. Protein contacts atlas gives non-covalent contacts framework by exploring interfaces of individual subunits and protein-ligand interactions. STRING tool predicts physical and functional interactions between proteins. The results of this study revealed that rutin and MG-132 could be promising inhibitors against targeted p53 protein and this could prove detrimental for molecular therapeutics and drug-designing strategies.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Bashir Ahmad Malla
- Department of Biochemistry, School of Biological Sciences, University of Kashmir, Srinagar, J&K, India
| | - Aarif Ali
- Department of Clinical Biochemistry, School of Biological Sciences, University of Kashmir, Srinagar, J&K, India
| | - Irfan Maqbool
- Department of Clinical Biochemistry, SKIMS Soura, Srinagar, J&K, India
| | - Nazir Ahmad Dar
- Department of Biochemistry, School of Biological Sciences, University of Kashmir, Srinagar, J&K, India
| | - Sheikh Bilal Ahmad
- Division of Veterinary Biochemistry, SKUAST-K, Shuhama Alusteng, J&K, India
| | - Rana M Alsaffar
- Department Of Pharmacology & Toxicology, College Of Pharmacy Girls Section, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Muneeb U Rehman
- Department of Clinical Pharmacy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
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47
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Li Y, Chen L, Li J, Zhao B, Jing T, Wang R. Computational explorations of the interaction between laccase and bisphenol A: influence of surfactant and different organic solvents. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2023; 34:963-981. [PMID: 38009185 DOI: 10.1080/1062936x.2023.2280584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 10/30/2023] [Indexed: 11/28/2023]
Abstract
Bisphenol A (BPA), as an environmental endocrine disruptor can cause damage to the reproductive, nervous and immune systems. Laccase can be used to degrade BPA. However, laccase is easily deactivated, especially in organic solvents, but the specific details are not clear. Molecular dynamics simulations were used to investigate the reasons for changes in laccase activity in acetonitrile (ACN) and dimethyl formamide (DMF) solutions. In addition, the effects of ACN and DMF on the activity of laccase and surfactant rhamnolipid (RL) on the degradation of BPA by laccase were investigated. Results showed that addition of ACN changed the structure of the laccase, not only decreasing the van der Waals interaction that promoted the binding of laccase with BPA, but also increasing the polar solvation free energy that hindered the binding of laccase with BPA, so it weakened the laccase activity. DMF greatly enhanced the van der Waals interaction between laccase and BPA, and played a positive role in their binding. The addition of surfactant RL alleviated the effect of organic solvent on the activity of laccase by changing the polar solvation energy. The mechanism of surfactant RL affecting laccase activity in ACN and DMF is described, providing support for understanding the effect of organic solvents on laccase.
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Affiliation(s)
- Y Li
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar, P. R. China
| | - L Chen
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar, P. R. China
| | - J Li
- Transportation Class in the first operation area of the Fourth Oil Production Plant of Daqing Oilfield of CNPC, Daqing, P. R. China
| | - B Zhao
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar, P. R. China
- Heilongjiang Provincial Key Laboratory of Surface Active Agent and Auxiliary, Qiqihar University, Qiqihar, P. R. China
| | - T Jing
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar, P. R. China
| | - R Wang
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar, P. R. China
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Adetunji JA, Ogunyemi OM, Gyebi GA, Adewumi AE, Olaiya CO. Atomistic simulations suggest dietary flavonoids from Beta vulgaris (beet) as promising inhibitors of human angiotensin-converting enzyme and 2-alpha-adrenergic receptors in hypertension. BIOINFORMATICS ADVANCES 2023; 3:vbad133. [PMID: 37822725 PMCID: PMC10562952 DOI: 10.1093/bioadv/vbad133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 09/08/2023] [Indexed: 10/13/2023]
Abstract
Motivation Beta vulgaris (beet) is extensively reported for its antihypertensive activity. However, the mechanismunderpinning its antihypertensive activity is not well understood. In this study, we evaluated the in silico interactionsof 70 compounds derived from beta vulgaris against the active sites of angiotensin-converting enzyme (ACE) and alpha-adrenergic receptor (AR). Results Structure-based virtual screening against angiotensin-converting enzyme revealed that, Cochliophilin A (-9.0 Kcal/mol), Miraxanthin (-8.3 Kcal/mol), and quercimeritrin (-9.7 Kcal/mol) had lower docking scores than the reference lisinopril (-7.9 Kcal/mol). These compounds exhibited dual binding tendency as they also ranked top compounds upon screening against adrenergic receptor. The thermodynamic parameters computed from the resulting trajectories obtained from the 100 ns full atomistic molecular dynamics simulation revealed structural stability and conformational flexibility of the ligand-receptor complexes as indicated by the RMSD, RMSF, RoG, SASA, and H-bond calculations. The molecular mechanics with generalized Born and surface area solvation binding energy calculations revealed that the proteins exhibit considerable binding energy with the phytochemicals in a dynamic environment. Furthermore, the hit compounds possess good physicochemical properties and drug-likeness. Overall, cochliophilin and quercimeritrin are promising dual-target directed flavonoids from Beta vulgaris; and are suggested for further experimental and preclinical evaluation. Availability and implementation All data was provided in the manuscript.
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Affiliation(s)
- Joy A Adetunji
- Nutritional and Industrial Biochemistry Laboratory, Department of Biochemistry, Faculty of Basic Medical Sciences, College of Medicine, University of Ibadan, Ibadan 200005, Nigeria
| | - Oludare M Ogunyemi
- Nutritional and Industrial Biochemistry Laboratory, Department of Biochemistry, Faculty of Basic Medical Sciences, College of Medicine, University of Ibadan, Ibadan 200005, Nigeria
| | - Gideon A Gyebi
- Department of Biochemistry, Faculty of Science and Technology, Bingham University, Karu, Nigeria
- Natural Products and Structural (Bio-Chem)-informatics Research Laboratory (NpsBC-Rl), Bingham University, Nasarawa, Nigeria
| | - Anuoluwapo E Adewumi
- Nutritional and Industrial Biochemistry Laboratory, Department of Biochemistry, Faculty of Basic Medical Sciences, College of Medicine, University of Ibadan, Ibadan 200005, Nigeria
| | - Charles O Olaiya
- Nutritional and Industrial Biochemistry Laboratory, Department of Biochemistry, Faculty of Basic Medical Sciences, College of Medicine, University of Ibadan, Ibadan 200005, Nigeria
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49
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Kurt M, Ercan S, Pirinccioglu N. Designing new drug candidates as inhibitors against wild and mutant type neuraminidases: molecular docking, molecular dynamics and binding free energy calculations. J Biomol Struct Dyn 2023; 41:7847-7861. [PMID: 36152997 DOI: 10.1080/07391102.2022.2125440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 09/12/2022] [Indexed: 10/14/2022]
Abstract
Influenza virus is the cause of the death of millions of people with about 3-4 pandemics every hundred years in history. It also turns into a seasonal disease, bringing about approximately 5-15% of the population to be infected and 290,000-650,000 people to die every year. These numbers reveal that it is necessary to be on the alert to work towards influenza in order to protect public health. There are FDA-approved antiviral drugs such as oseltamivir and zanamivir recommended by the World Center for Disease Prevention. However, after the recent outbreaks such as bird flu and swine flu, increasing studies have shown that the flu virus has gained resistance to these drugs. So, there is an urgent need to find new drugs effective against this virus. This study aims to investigate new drug candidates targeting neuraminidase (NA) for the treatment of influenza by using computer aided drug design approaches. They involve virtual scanning, de novo design, rational design, docking, MD, MMGB/PBSA. The investigation includes H1N1, H5N1, H2N2 and H3N2 neuraminidase proteins and their mutant variants possessing resistance to FDA-approved drugs. Virtual screening consists of approximately 30 thousand molecules while de novo and rational designs produced over a hundred molecules. These approaches produced three lead molecules with binding energies for both non-mutant (-34.84, -59.99 and -60.66 kcal/mol) and mutant (-40.40, -58.93, -76.19 kcal/mol) H2N2 NA calculated by MM-PBSA compared with those of oseltamivir -25.64 and -18.40 respectively. The results offer new drug candidates against influenza infection.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Murat Kurt
- Institute of Science, Dicle University, Diyarbakır, Turkey
| | - Selami Ercan
- Department of Chemistry, Batman University, Batman, Turkey
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50
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Sisodia R, Mazumdar PA, Madhurantakam C. In silico identification and analysis of potential inhibitors for acid phosphatase, HppA from Helicobacter pylori. J Mol Recognit 2023; 36:e3049. [PMID: 37553866 DOI: 10.1002/jmr.3049] [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: 03/30/2023] [Revised: 07/20/2023] [Accepted: 07/21/2023] [Indexed: 08/10/2023]
Abstract
Helicobacter pylori is the most common cause of gastric ulcers and is associated with gastric cancer. The enzyme HppA of class C nonspecific acid phosphohydrolases (NSAPs) of H. pylori plays a crucial role in the electron transport chain. Herein, we report an in silico homology model of HppA consisting of a monomeric α + β model. A high throughput structure-based virtual screening approach yielded potential inhibitors against HppA with higher binding energies. Further analyses of molecular interaction maps and protein-ligand fingerprints, followed by molecular mechanics-generalized Born surface area (MM-GBSA) end point binding energy calculations of docked complexes, resulted in the detection of top binders/ligands. Our investigations identified potential substrate-competitive small molecule inhibitors of HppA, with admissible pharmacokinetic properties. These molecules may provide a starting point for developing novel therapeutic agents against H. pylori.
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Affiliation(s)
- Rinki Sisodia
- Structural and Molecular Biology Laboratory (SMBL), Department of Biotechnology, TERI School of Advanced Studies (TERI SAS), New Delhi, India
| | | | - Chaithanya Madhurantakam
- Structural and Molecular Biology Laboratory (SMBL), Department of Biotechnology, TERI School of Advanced Studies (TERI SAS), New Delhi, India
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