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Mitchell SM, Heise RM, Murray ME, Lambo DJ, Daso RE, Banerjee IA. An investigation of binding interactions of tumor-targeted peptide conjugated polyphenols with the kinase domain of ephrin B4 and B2 receptors. Mol Divers 2024; 28:817-849. [PMID: 36847923 PMCID: PMC9969393 DOI: 10.1007/s11030-023-10621-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 02/02/2023] [Indexed: 03/01/2023]
Abstract
Recent studies have shown that Ephrin receptors may be upregulated in several types of cancers including breast, ovarian and endometrial cancers, making them a target for drug design. In this work, we have utilized a target-hopping approach to design new natural product-peptide conjugates and examined their interactions with the kinase-binding domain of EphB4 and EphB2 receptors. The peptide sequences were generated through point mutations of the known EphB4 antagonist peptide TNYLFSPNGPIA. Their anticancer properties and secondary structures were analyzed computationally. Conjugates of most optimum of peptides were then designed by binding the N-terminal of the peptides with the free carboxyl group of the polyphenols sinapate, gallate and coumarate, which are known for their inherent anticancer properties. To investigate if these conjugates have a potential to bind to the kinase domain, we carried out docking studies and MMGBSA free energy calculations of the trajectories based on the molecular dynamics simulations, with both the apo and the ATP bound kinase domains of both receptors. In most cases binding interactions occurred within the catalytic loop region, while in some cases the conjugates were found to spread out across the N-lobe and the DFG motif region. The conjugates were further tested for prediction of pharmacokinetic properties using ADME studies. Our results indicated that the conjugates were lipophilic and MDCK permeable with no CYP interactions. These findings provide an insight into the molecular interactions of these peptides and conjugates with the kinase domain of the EphB4 and EphB2 receptor. As a proof of concept, we synthesized and carried out SPR analysis with two of the conjugates (gallate-TNYLFSPNGPIA and sinapate-TNYLFSPNGPIA). Results indicated that the conjugates showed higher binding with the EphB4 receptor and minimal binding to EphB2 receptor. Sinapate-TNYLFSPNGPIA showed inhibitory activity against EphB4. These studies reveal that some of the conjugates may be developed for further investigation into in vitro and in vivo studies and potential development as therapeutics.
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Affiliation(s)
- Saige M Mitchell
- Department of Chemistry, Fordham University, 441 E. Fordham Rd, Bronx, NY, 10458, USA
| | - Ryan M Heise
- Department of Chemistry, Fordham University, 441 E. Fordham Rd, Bronx, NY, 10458, USA
| | - Molly E Murray
- Department of Chemistry, Fordham University, 441 E. Fordham Rd, Bronx, NY, 10458, USA
| | - Dominic J Lambo
- Department of Chemistry, Fordham University, 441 E. Fordham Rd, Bronx, NY, 10458, USA
| | - Rachel E Daso
- Department of Chemistry, Fordham University, 441 E. Fordham Rd, Bronx, NY, 10458, USA
| | - Ipsita A Banerjee
- Department of Chemistry, Fordham University, 441 E. Fordham Rd, Bronx, NY, 10458, USA.
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Durai P, Lee SJ, Lee JW, Pan CH, Park K. Iterative machine learning-based chemical similarity search to identify novel chemical inhibitors. J Cheminform 2023; 15:86. [PMID: 37742003 PMCID: PMC10517535 DOI: 10.1186/s13321-023-00760-6] [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: 05/23/2023] [Accepted: 09/12/2023] [Indexed: 09/25/2023] Open
Abstract
Machine learning-based chemical screening has made substantial progress in recent years. However, these predictions often have low accuracy and high uncertainty when identifying new active chemical scaffolds. Hence, a high proportion of retrieved compounds are not structurally novel. In this study, we proposed a strategy to address this issue by iteratively optimizing an evolutionary chemical binding similarity (ECBS) model using experimental validation data. Various data update and model retraining schemes were tested to efficiently incorporate new experimental data into ECBS models, resulting in a fine-tuned ECBS model with improved accuracy and coverage. To demonstrate the effectiveness of our approach, we identified the novel hit molecules for the mitogen-activated protein kinase kinase 1 (MEK1). These molecules showed sub-micromolar affinity (Kd 0.1-5.3 μM) to MEKs and were distinct from previously-known MEK1 inhibitors. We also determined the binding specificity of different MEK isoforms and proposed potential docking models. Furthermore, using de novo drug design tools, we utilized one of the new MEK inhibitors to generate additional drug-like molecules with improved binding scores. This resulted in the identification of several potential MEK1 inhibitors with better binding affinity scores. Our results demonstrated the potential of this approach for identifying novel hit molecules and optimizing their binding affinities.
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Affiliation(s)
- Prasannavenkatesh Durai
- Natural Product Informatics Research Center, Korea Institute of Science and Technology, Gangneung, 25451, Republic of Korea
| | - Sue Jung Lee
- Natural Product Research Center, Korea Institute of Science and Technology, Gangneung, 25451, Republic of Korea
| | - Jae Wook Lee
- Natural Product Research Center, Korea Institute of Science and Technology, Gangneung, 25451, Republic of Korea
| | - Cheol-Ho Pan
- Natural Product Informatics Research Center, Korea Institute of Science and Technology, Gangneung, 25451, Republic of Korea
| | - Keunwan Park
- Natural Product Informatics Research Center, Korea Institute of Science and Technology, Gangneung, 25451, Republic of Korea.
- Department of YM-KIST Bio-Health Convergence, Yonsei University, Wonju, 26493, Republic of Korea.
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Halayal RY, Bagewadi ZK, Maliger RB, Al Jadidi S, Deshpande SH. Network pharmacology based anti-diabetic attributes of bioactive compounds from Ocimum gratissimum L . through computational approach. Saudi J Biol Sci 2023; 30:103766. [PMID: 37588570 PMCID: PMC10425415 DOI: 10.1016/j.sjbs.2023.103766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 07/26/2023] [Accepted: 07/29/2023] [Indexed: 08/18/2023] Open
Abstract
The present research was framed to determine the key compounds present in the plant Ocimum gratissimum L. targeting protein molecules of Diabetes Mellitus (DM) by employing In-silico approaches. Phytochemicals previously reported to be present in this herb were collated through literature survey and public phytochemical databases, and their probable targets were anticipated using BindingDB (p ≥ 0.7). STRING and KEGG pathway databases were employed for pathway enrichment analysis. Homology modelling was executed to elucidate the structures of therapeutic targets. Further, Phytocompounds from O. gratissimum were subjected for docking with four therapeutic targets of DM by using AutoDock vina through POAP pipeline implementation. 30 compounds were predicted to target 136 protein molecules including aldose reductase, DPP4, alpha-amylase, and alpha-glucosidase. Neuroactive ligand-receptor interaction, MAPK, PI3K-Akt, starch and insulin resistance were predicted to have potentially modulation by phytocompounds. Based on the phytocompound's binding score with the four targets of DM, Rutin scored the lowest binding energy (-11 kcal/mol) with Aldose reductase by forming 17 intermolecular interactions. In conclusion, based on the network and binding score, phytocompounds from O. gratissimum have a synergistic and considerable effect in the management of DM via multi-compound, multi-target, and multi-pathway mechanisms.
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Affiliation(s)
- Rekha Y. Halayal
- Department of Biotechnology, KLE Technological University, Hubballi, Karnataka 580031, India
| | - Zabin K. Bagewadi
- Department of Biotechnology, KLE Technological University, Hubballi, Karnataka 580031, India
| | - Raju B. Maliger
- Department of Mechanical and Industrial Engineering (MIE), University of Technology & Applied Sciences, Muscat, Oman
| | - Salim Al Jadidi
- Department of Mechanical and Industrial Engineering (MIE), University of Technology & Applied Sciences, Muscat, Oman
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Titov IY, Stroylov VS, Rusina P, Svitanko IV. Preliminary modelling as the first stage of targeted organic synthesis. RUSSIAN CHEMICAL REVIEWS 2021. [DOI: 10.1070/rcr5012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The review aims to present a classification and applicability analysis of methods for preliminary molecular modelling for targeted organic, catalytic and biocatalytic synthesis. The following three main approaches are considered as a primary classification of the methods: modelling of the target – ligand coordination without structural information on both the target and the resulting complex; calculations based on experimentally obtained structural information about the target; and dynamic simulation of the target – ligand complex and the reaction mechanism with calculation of the free energy of the reaction. The review is meant for synthetic chemists to be used as a guide for building an algorithm for preliminary modelling and synthesis of structures with specified properties.
The bibliography includes 353 references.
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Wang K, Chen Q, Liu N, Zhang J, Pan X. Recent advances in, and challenges of, anti-angiogenesis agents for tumor chemotherapy based on vascular normalization. Drug Discov Today 2021; 26:2743-2753. [PMID: 34332098 DOI: 10.1016/j.drudis.2021.07.024] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 07/02/2021] [Accepted: 07/06/2021] [Indexed: 12/18/2022]
Abstract
A major problem associated with cancer treatment is resistance-prone chemotherapeutic drugs. An increasing number of studies have documented that the occurrence of resistance tends to be associated with abnormal blood vessels. In 2001, Jain proposed the vascular normalization theory, which was recently applied to the drug-resistant treatment of tumors in the clinic. Through the intervention of angiogenesis inhibitors, remodeling the structure and function of abnormal vessels can maximize the efficacy of chemotherapeutic drugs. In this review, we systematically describe the occurrence and progress of tumor angiogenesis, as well as the pathological characteristics of tumor blood vessels. Moreover, druggable targets for vascular normalization and the development of related inhibitors are also outlined.
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Affiliation(s)
- Kai Wang
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an 710061, China
| | - Qinhua Chen
- Department of Pharmacy, Shenzhen Baoan Authentic TCM Therapy Hospital, Shenzhen 518101, China
| | - Nanxin Liu
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an 710061, China
| | - Jie Zhang
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an 710061, China
| | - Xiaoyan Pan
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an 710061, China.
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Park JS, Ko K, Kim SH, Lee JK, Park JS, Park K, Kim MR, Kang K, Oh DC, Kim SY, Yumnam S, Kwon HC, Shin J. Tropolone-Bearing Sesquiterpenes from Juniperus chinensis: Structures, Photochemistry and Bioactivity. JOURNAL OF NATURAL PRODUCTS 2021; 84:2020-2027. [PMID: 34236881 DOI: 10.1021/acs.jnatprod.1c00321] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The tropolone-bearing sesquiterpenes juniperone A (1) and norjuniperone A (2) were isolated from the folk medicinal plant Juniperus chinensis, and their structures were determined by a combination of spectroscopic and crystallographic methods. Photojuniperones A1 (3) and A2 (4), bearing bicyclo[3,2,0]heptadienones derived from tropolone, were photochemically produced and structurally identified by spectroscopic methods. Predicted by the machine learning-based assay, 1 significantly inhibited the action of tyrosinase. The new compounds also inhibited lipid accumulation and enhanced the extracellular glycerol excretion.
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Affiliation(s)
- Jae Sung Park
- Natural Products Research Institute, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Keebeom Ko
- Natural Products Research Institute, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Seong-Hwan Kim
- Natural Product Informatics Research Center, Korea Institute of Science and Technology (KIST) Gangneung Institute, Gangneung 25451, Republic of Korea
| | - Jae Kyun Lee
- Neuro-Medicine, Korea Institute of Science and Technology, Hwarang-ro 14-gil 5, Seongbuk-gu, Seoul 02792, Republic of Korea
| | - Jin-Soo Park
- Natural Product Informatics Research Center, Korea Institute of Science and Technology (KIST) Gangneung Institute, Gangneung 25451, Republic of Korea
| | - Keunwan Park
- Natural Product Informatics Research Center, Korea Institute of Science and Technology (KIST) Gangneung Institute, Gangneung 25451, Republic of Korea
| | - Mi Ri Kim
- Natural Product Informatics Research Center, Korea Institute of Science and Technology (KIST) Gangneung Institute, Gangneung 25451, Republic of Korea
| | - Kyungsu Kang
- Natural Product Informatics Research Center, Korea Institute of Science and Technology (KIST) Gangneung Institute, Gangneung 25451, Republic of Korea
| | - Dong-Chan Oh
- Natural Products Research Institute, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Sun Yeou Kim
- Gachon Institute of Pharmaceutical Science, Gachon University, 191, Hambakmoe-ro, Yeonsu-gu, Incheon 21936, Republic of Korea
| | - Silvia Yumnam
- Gachon Institute of Pharmaceutical Science, Gachon University, 191, Hambakmoe-ro, Yeonsu-gu, Incheon 21936, Republic of Korea
| | - Hak Cheol Kwon
- Natural Product Informatics Research Center, Korea Institute of Science and Technology (KIST) Gangneung Institute, Gangneung 25451, Republic of Korea
| | - Jongheon Shin
- Natural Products Research Institute, College of Pharmacy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
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Li X, Munir S, Xu Y, Wang Y, He Y. Combined mass spectrometry-guided genome mining and virtual screening for acaricidal activity in secondary metabolites of Bacillus velezensis W1. RSC Adv 2021; 11:25441-25449. [PMID: 35478879 PMCID: PMC9037071 DOI: 10.1039/d1ra01326b] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 07/12/2021] [Indexed: 11/21/2022] Open
Abstract
A comprehensive analytic strategy was performed to study the acaricidal activity ingredients of Bacillus velezensis W1, a strain for biological control of Tetranychus urticae. Through genome mining, 14 biosynthetic gene clusters were identified, which encode secondary metabolites, and these were further confirmed by MALDI-TOF-MS or LC-ESI-MS/MS, including bacillomycin D C13–C17, macrolactin A, 7-O-malonyl-macrolactin A, surfactin C14, and surfactin C15. Moreover, 27 volatile compounds were identified by GC-MS, mainly including cyclodipeptides, alkanes, organic acids, and esters. Finally, 43 compounds identified from W1 were used in the virtual screening of acaricidal activity. The results showed that 16 compounds, including cyclodipeptides, bacillomycins, macrolactins, and surfactins, have acaricidal potential. This work provides a base for studying the mechanism of acaricidal action of B. velezensis W1 and a comprehensive strategy for the study of active ingredients from biocontrol strains. A comprehensive analytic strategy was performed to study the acaricidal activity ingredients of Bacillus velezensis W1, a strain for biological control of Tetranychus urticae.![]()
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Affiliation(s)
- Xingyu Li
- College of Science, Yunnan Agricultural University Kunming 650201 China .,Department of Chemistry, Cleveland State University Cleveland OH 44115 USA
| | - Shahzad Munir
- State Key Laboratory for Conservation and Utilization of Bio-resources in Yunnan, Yunnan Agricultural University Kunming 650201 Yunnan China
| | - Yan Xu
- Department of Chemistry, Cleveland State University Cleveland OH 44115 USA
| | - Yuehu Wang
- Key Laboratory of Economic Plants and Biotechnology, Chinese Academy of Sciences Kunming 650201 China
| | - Yueqiu He
- State Key Laboratory for Conservation and Utilization of Bio-resources in Yunnan, Yunnan Agricultural University Kunming 650201 Yunnan China
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Durai P, Ko YJ, Kim JC, Pan CH, Park K. Identification of Tyrosinase Inhibitors and Their Structure-Activity Relationships via Evolutionary Chemical Binding Similarity and Structure-Based Methods. Molecules 2021; 26:molecules26030566. [PMID: 33499015 PMCID: PMC7865271 DOI: 10.3390/molecules26030566] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/19/2021] [Accepted: 01/20/2021] [Indexed: 12/17/2022] Open
Abstract
Tyrosinase is an enzyme that plays a crucial role in the melanogenesis of humans and the browning of food products. Thus, tyrosinase inhibitors that are useful to the cosmetic and food industries are required. In this study, we have used evolutionary chemical binding similarity (ECBS) to screen a virtual chemical database for human tyrosinase, which resulted in seven potential tyrosinase inhibitors confirmed through the tyrosinase inhibition assay. The tyrosinase inhibition percentage for three of the new actives was over 90% compared to 61.9% of kojic acid. From the structural analysis through pharmacophore modeling and molecular docking with the human tyrosinase model, the pi–pi interaction of tyrosinase inhibitors with conserved His367 and the polar interactions with Asn364, Glu345, and Glu203 were found to be essential for tyrosinase–ligand interactions. The pharmacophore features and the docking models showed high consistency, revealing the possible essential binding interactions of inhibitors to human tyrosinase. We have also presented the activity cliff analysis that successfully revealed the chemical features related to substantial activity changes found in the new tyrosinase inhibitors. The newly identified inhibitors and their structure–activity relationships presented here will help to identify or design new human tyrosinase inhibitors.
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Affiliation(s)
- Prasannavenkatesh Durai
- Natural Product Informatics Research Center, KIST Gangneung Institute of Natural Products, Gangneung 25451, Korea; (P.D.); (Y.-J.K.); (J.-C.K.); (C.-H.P.)
| | - Young-Joon Ko
- Natural Product Informatics Research Center, KIST Gangneung Institute of Natural Products, Gangneung 25451, Korea; (P.D.); (Y.-J.K.); (J.-C.K.); (C.-H.P.)
- Department of Bioinformatics and Life Science, Soongsil University, Seoul 06978, Korea
| | - Jin-Chul Kim
- Natural Product Informatics Research Center, KIST Gangneung Institute of Natural Products, Gangneung 25451, Korea; (P.D.); (Y.-J.K.); (J.-C.K.); (C.-H.P.)
| | - Cheol-Ho Pan
- Natural Product Informatics Research Center, KIST Gangneung Institute of Natural Products, Gangneung 25451, Korea; (P.D.); (Y.-J.K.); (J.-C.K.); (C.-H.P.)
| | - Keunwan Park
- Natural Product Informatics Research Center, KIST Gangneung Institute of Natural Products, Gangneung 25451, Korea; (P.D.); (Y.-J.K.); (J.-C.K.); (C.-H.P.)
- Correspondence: ; Tel.: +82-33-650-3663
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