1
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Elseginy SA. Identifying and characterising promising small molecule inhibitors of kinesin spindle protein using ligand-based virtual screening, molecular docking, molecular dynamics and MM‑GBSA calculations. J Comput Aided Mol Des 2024; 38:16. [PMID: 38556596 PMCID: PMC10982093 DOI: 10.1007/s10822-024-00553-5] [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: 12/28/2023] [Accepted: 02/22/2024] [Indexed: 04/02/2024]
Abstract
The kinesin spindle protein (Eg5) is a mitotic protein that plays an essential role in the formation of the bipolar spindles during the mitotic phase. Eg5 protein controls the segregation of the chromosomes in mitosis which renders it a vital target for cancer treatment. In this study our approach to identifying novel scaffold for Eg5 inhibitors is based on targeting the novel allosteric pocket (α4/α6/L11). Extensive computational techniques were applied using ligand-based virtual screening and molecular docking by two approaches, MOE and AutoDock, to screen a library of commercial compounds. We identified compound 8-(3-(1H-imidazol-1-ylpropylamino)-3-methyl-7-((naphthalen-3-yl)methyl)-1H-purine-2, 6 (3H,7H)-dione (compound 5) as a novel scaffold for Eg5 inhibitors. This compound inhibited cancer cell Eg5 ATPase at 2.37 ± 0.15 µM. The molecular dynamics simulations revealed that the identified compound formed stable interactions in the allosteric pocket (α4/α6/L11) of the receptor, indicating its potential as a novel Eg5 inhibitor.
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Affiliation(s)
- Samia A Elseginy
- Chemical Industries Research Division, Green Chemistry Department, National Research Centre, Cairo, 12622, Egypt.
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2
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Guo W, Du D, Zhang H, Sanchez JE, Sun S, Xu W, Peng Y, Li L. Bound ion effects: Using machine learning method to study the kinesin Ncd's binding with microtubule. Biophys J 2023:S0006-3495(23)04176-0. [PMID: 38160255 DOI: 10.1016/j.bpj.2023.12.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 11/26/2023] [Accepted: 12/27/2023] [Indexed: 01/03/2024] Open
Abstract
Drosophila Ncd proteins are motor proteins that play important roles in spindle organization. Ncd and the tubulin dimer are highly charged. Thus, it is crucial to investigate Ncd-tubulin dimer interactions in the presence of ions, especially ions that are bound or restricted at the Ncd-tubulin dimer binding interfaces. To consider the ion effects, widely used implicit solvent models treat ions implicitly in the continuous solvent environment without focusing on the individual ions' effects. But highly charged biomolecules such as the Ncd and tubulin dimer may capture some ions at highly charged regions as bound ions. Such bound ions are restricted to their binding sites; thus, they can be treated as part of the biomolecules. By applying multiscale computational methods, including the machine-learning-based Hybridizing Ions Treatment-2 program, molecular dynamics simulations, DelPhi, and DelPhiForce, we studied the interaction between the Ncd motor domain and the tubulin dimer using a hybrid solvent model, which considers the bound ions explicitly and the other ions implicitly in the solvent environment. To identify the importance of treating bound ions explicitly, we also performed calculations using the implicit solvent model without considering the individual bound ions. We found that the calculations of the electrostatic features differ significantly between those of the hybrid solvent model and the pure implicit solvent model. The analyses show that treating bound ions at highly charged regions explicitly is crucial for electrostatic calculations. This work proposes a machine-learning-based approach to handle the bound ions using the hybrid solvent model. Such an approach is not only capable of handling kinesin-tubulin complexes but is also appropriate for other highly charged biomolecules, such as DNA/RNA, viral capsid proteins, etc.
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Affiliation(s)
- Wenhan Guo
- College of Physical Science and Technology, Central China Normal University, Hubei, China; Computational Science Program, University of Texas at El Paso, El Paso, Texas
| | - Dan Du
- Computational Science Program, University of Texas at El Paso, El Paso, Texas
| | - Houfang Zhang
- College of Physical Science and Technology, Central China Normal University, Hubei, China
| | - Jason E Sanchez
- Computational Science Program, University of Texas at El Paso, El Paso, Texas
| | - Shengjie Sun
- Computational Science Program, University of Texas at El Paso, El Paso, Texas; School of Life Sciences, Central South University, Hunan, China
| | - Wang Xu
- College of Physical Science and Technology, Central China Normal University, Hubei, China
| | - Yunhui Peng
- College of Physical Science and Technology, Central China Normal University, Hubei, China.
| | - Lin Li
- Computational Science Program, University of Texas at El Paso, El Paso, Texas; Department of Physics, University of Texas at El Paso, El Paso, Texas.
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3
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Sharma N, Setiawan D, Hamelberg D, Narayan R, Aneja R. Computational benchmarking of putative KIFC1 inhibitors. Med Res Rev 2023; 43:293-318. [PMID: 36104980 DOI: 10.1002/med.21926] [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: 11/25/2021] [Revised: 08/06/2022] [Accepted: 08/17/2022] [Indexed: 02/05/2023]
Abstract
The centrosome in animal cells is instrumental in spindle pole formation, nucleation, proper alignment of microtubules during cell division, and distribution of chromosomes in each daughter cell. Centrosome amplification involving structural and numerical abnormalities in the centrosome can cause chromosomal instability and dysregulation of the cell cycle, leading to cancer development and metastasis. However, disturbances caused by centrosome amplification can also limit cancer cell survival by activating mitotic checkpoints and promoting mitotic catastrophe. As a smart escape, cancer cells cluster their surplus of centrosomes into pseudo-bipolar spindles and progress through the cell cycle. This phenomenon, known as centrosome clustering (CC), involves many proteins and has garnered considerable attention as a specific cancer cell-targeting weapon. The kinesin-14 motor protein KIFC1 is a minus end-directed motor protein that is involved in CC. Because KIFC1 is upregulated in various cancers and modulates oncogenic signaling cascades, it has emerged as a potential chemotherapeutic target. Many molecules have been identified as KIFC1 inhibitors because of their centrosome declustering activity in cancer cells. Despite the ever-increasing literature in this field, there have been few efforts to review the progress. The current review aims to collate and present an in-depth analysis of known KIFC1 inhibitors and their biological activities. Additionally, we present computational docking data of putative KIFC1 inhibitors with their binding sites and binding affinities. This first-of-kind comparative analysis involving experimental biology, chemistry, and computational docking of different KIFC1 inhibitors may help guide decision-making in the selection and design of potent inhibitors.
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Affiliation(s)
- Nivya Sharma
- Department of Biology, Georgia State University, Atlanta, Georgia, USA
| | - Dani Setiawan
- Department of Chemistry, Georgia State University, Atlanta, Georgia, USA
| | - Donald Hamelberg
- Department of Chemistry, Georgia State University, Atlanta, Georgia, USA
| | - Rishikesh Narayan
- School of Chemical and Materials Sciences, Indian Institute of Technology Goa, Goa, India.,School of Interdisciplinary Life Sciences, Indian Institute of Technology Goa, Goa, India
| | - Ritu Aneja
- Department of Biology, Georgia State University, Atlanta, Georgia, USA.,Department of Clinical and Diagnostic Sciences, School of Health Professions, University of Alabama at Birmingham, Birmingham, AL, USA
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4
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Saint-Dizier F, Matthews TP, Gregson AM, Prevet H, McHardy T, Colombano G, Saville H, Rowlands M, Ewens C, McAndrew PC, Tomlin K, Guillotin D, Mak GWY, Drosopoulos K, Poursaitidis I, Burke R, van Montfort R, Linardopoulos S, Collins I. Discovery of 2-(3-Benzamidopropanamido)thiazole-5-carboxylate Inhibitors of the Kinesin HSET (KIFC1) and the Development of Cellular Target Engagement Probes. J Med Chem 2023; 66:2622-2645. [PMID: 36749938 PMCID: PMC9969401 DOI: 10.1021/acs.jmedchem.2c01591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Indexed: 02/09/2023]
Abstract
The existence of multiple centrosomes in some cancer cells can lead to cell death through the formation of multipolar mitotic spindles and consequent aberrant cell division. Many cancer cells rely on HSET (KIFC1) to cluster the extra centrosomes into two groups to mimic the bipolar spindle formation of non-centrosome-amplified cells and ensure their survival. Here, we report the discovery of a novel 2-(3-benzamidopropanamido)thiazole-5-carboxylate with micromolar in vitro inhibition of HSET (KIFC1) through high-throughput screening and its progression to ATP-competitive compounds with nanomolar biochemical potency and high selectivity against the opposing mitotic kinesin Eg5. Induction of the multipolar phenotype was shown in centrosome-amplified human cancer cells treated with these inhibitors. In addition, a suitable linker position was identified to allow the synthesis of both fluorescent- and trans-cyclooctene (TCO)-tagged probes, which demonstrated direct compound binding to the HSET protein and confirmed target engagement in cells, through a click-chemistry approach.
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Affiliation(s)
- François Saint-Dizier
- Centre
for Cancer Drug Discovery, Division of Cancer Therapeutics, The Institute of Cancer Research, London SW7 3RP, U.K.
| | - Thomas P. Matthews
- Centre
for Cancer Drug Discovery, Division of Cancer Therapeutics, The Institute of Cancer Research, London SW7 3RP, U.K.
| | - Aaron M. Gregson
- Centre
for Cancer Drug Discovery, Division of Cancer Therapeutics, The Institute of Cancer Research, London SW7 3RP, U.K.
| | - Hugues Prevet
- Centre
for Cancer Drug Discovery, Division of Cancer Therapeutics, The Institute of Cancer Research, London SW7 3RP, U.K.
| | - Tatiana McHardy
- Centre
for Cancer Drug Discovery, Division of Cancer Therapeutics, The Institute of Cancer Research, London SW7 3RP, U.K.
| | - Giampiero Colombano
- Centre
for Cancer Drug Discovery, Division of Cancer Therapeutics, The Institute of Cancer Research, London SW7 3RP, U.K.
| | - Harry Saville
- Centre
for Cancer Drug Discovery, Division of Cancer Therapeutics, The Institute of Cancer Research, London SW7 3RP, U.K.
| | - Martin Rowlands
- Centre
for Cancer Drug Discovery, Division of Cancer Therapeutics, The Institute of Cancer Research, London SW7 3RP, U.K.
| | - Caroline Ewens
- Centre
for Cancer Drug Discovery, Division of Cancer Therapeutics, The Institute of Cancer Research, London SW7 3RP, U.K.
| | - P. Craig McAndrew
- Centre
for Cancer Drug Discovery, Division of Cancer Therapeutics, The Institute of Cancer Research, London SW7 3RP, U.K.
| | - Kathy Tomlin
- Centre
for Cancer Drug Discovery, Division of Cancer Therapeutics, The Institute of Cancer Research, London SW7 3RP, U.K.
| | - Delphine Guillotin
- Centre
for Cancer Drug Discovery, Division of Cancer Therapeutics, The Institute of Cancer Research, London SW7 3RP, U.K.
| | - Grace Wing-Yan Mak
- Centre
for Cancer Drug Discovery, Division of Cancer Therapeutics, The Institute of Cancer Research, London SW7 3RP, U.K.
| | | | - Ioannis Poursaitidis
- Centre
for Cancer Drug Discovery, Division of Cancer Therapeutics, The Institute of Cancer Research, London SW7 3RP, U.K.
| | - Rosemary Burke
- Centre
for Cancer Drug Discovery, Division of Cancer Therapeutics, The Institute of Cancer Research, London SW7 3RP, U.K.
| | - Rob van Montfort
- Centre
for Cancer Drug Discovery, Division of Cancer Therapeutics, The Institute of Cancer Research, London SW7 3RP, U.K.
- Division
of Structural Biology, The Institute of
Cancer Research, London SW7 3RP, U.K.
| | - Spiros Linardopoulos
- Centre
for Cancer Drug Discovery, Division of Cancer Therapeutics, The Institute of Cancer Research, London SW7 3RP, U.K.
- Breast
Cancer Now Research Centre, The Institute of Cancer Research, London SW7 3RP, U.K.
| | - Ian Collins
- Centre
for Cancer Drug Discovery, Division of Cancer Therapeutics, The Institute of Cancer Research, London SW7 3RP, U.K.
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5
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Anchoring geometry is a significant factor in determining the direction of kinesin-14 motility on microtubules. Sci Rep 2022; 12:15417. [PMID: 36104376 PMCID: PMC9474454 DOI: 10.1038/s41598-022-19589-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 08/31/2022] [Indexed: 11/25/2022] Open
Abstract
Kinesin-14 microtubule-based motors have an N-terminal tail attaching the catalytic core to its load and usually move towards microtubule minus ends, whilst most other kinesins have a C-terminal tail and move towards plus ends. Loss of conserved sequences external to the motor domain causes kinesin-14 to switch to plus-end motility, showing that an N-terminal attachment is compatible with plus-end motility. However, there has been no systematic study on the role of attachment position in minus-end motility. We therefore examined the motility of monomeric kinesin-14s differing only in their attachment point. We find that a C-terminal attachment point causes kinesin-14s to become plus-end-directed, with microtubule corkscrewing rotation direction and pitch in motility assays similar to that of kinesin-1, suggesting that both C-kinesin kinesins-14 and N-kinesin kinesin-1 share a highly conserved catalytic core function with an intrinsic plus-end bias. Thus, an N-terminal attachment is one of the requirements for minus-end motility in kinesin-14.
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6
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Khan MKA, Ahmad S, Rabbani G, Shahab U, Khan MS. Target-based virtual screening, computational multiscoring docking and molecular dynamics simulation of small molecules as promising drug candidate affecting kinesin-like protein KIFC1. Cell Biochem Funct 2022; 40:451-472. [PMID: 35758564 DOI: 10.1002/cbf.3707] [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: 03/26/2022] [Revised: 04/28/2022] [Accepted: 05/04/2022] [Indexed: 11/07/2022]
Abstract
The kinesin family member C1 (KIFC1) is an essential protein that facilitates the bipolar division of neoplastic cells. Inhibiting KIFC1 by small molecules is a lucrative strategy to impede bipolar mitosis leading to the apoptosis of cancerous cells. The research aims to envisage small-molecule inhibitors targeting KIFC1. The Mcule database, a comprehensive online digital platform containing more than five million chemical compounds, was used for structure-based virtual screening (SBVS). Druglikeness filtration sifted 2,293,282 chemical hits that further narrowed down to 49 molecules after toxicity profiling. Finally, 39 compounds that comply with the BOILED-Egg permeation predictive model of the ADME rules were carried forward for multiscoring docking using the AutoDock Vina inbuilt to Mcule drug discovery platform, DockThor and SwissDock tools. The mean of ΔG terms produced by docking tools was computed to find consensus top ligand hits. AZ82 exhibited stronger binding (Consensus ΔG: -7.99 kcal mol-1 ) with KIFC1 among reference inhibitors, for example, CW069 (-7.57 kcal mol-1 ) and SR31527 (-7.01 kcal mol-1 ). Ten ligand hits namely, Mcule-4895338547 (Consensus ΔG: -8.69 kcal mol-1 ), Mcule-7035674888 (-8.42 kcal mol-1 ), Mcule-5531166845 (-8.53 kcal mol-1 ), Mcule-3248415882 (-8.55 kcal mol-1 ), Mcule-291881733 (-8.41 kcal mol-1 ), Mcule-5918624394 (-8.44), Mcule-3470115427 (-8.47), Mcule-3686193135 (-8.18 kcal mol-1 ), Mcule-3955355291 (8.09 kcal mol-1 ) and Mcule-9534899193 (-8.01 kcal mol-1 ) depicted strong binding interactions with KIFC1 in comparison to potential reference inhibitor AZ82. The top four ligands and AZ82 were considered for molecular dynamics simulation of 50 ns duration. Toxicity profiling, physicochemical properties, lipophilicity, solubility, pharmacokinetics, druglikeness, medicinal chemistry attributes, average potential energy, RMSD, RMSF, SASA, ΔGsolv and Rg analyses forecast the ligand mcule-4895338547 as a promising inhibitor of KIFC1.
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Affiliation(s)
| | - Saheem Ahmad
- Department of Biosciences, Integral University, Lucknow, India
| | - Gulam Rabbani
- Nano Diagnostics & Devices (NDD), IT Medical Fusion Center, Gumi-si, Gyeongbuk, Republic of Korea
| | - Uzma Shahab
- Department of Biotechnology, KMC Language University, Lucknow, India
| | - Mohd Shahnawaz Khan
- Department of Biochemistry, College of Sciences, King Saud University, Riyadh, Kingdom of Saudi Arabia
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7
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Tamayo NA, Bourbeau MP, Allen JR, Ashton KS, Chen JJ, Kaller MR, Nguyen TT, Nishimura N, Pettus LH, Walton M, Belmontes B, Moriguchi J, Chen K, McCarter JD, Hanestad K, Chung G, Ninniri MSS, Sun J, Poppe L, Spahr C, Hui J, Jia L, Wu T, Dahal UP, Edson KZ, Payton M. Targeting the Mitotic Kinesin KIF18A in Chromosomally Unstable Cancers: Hit Optimization Toward an In Vivo Chemical Probe. J Med Chem 2022; 65:4972-4990. [PMID: 35286090 DOI: 10.1021/acs.jmedchem.1c02030] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Chromosomal instability (CIN) is a hallmark of cancer that results from errors in chromosome segregation during mitosis. Targeting of CIN-associated vulnerabilities is an emerging therapeutic strategy in drug development. KIF18A, a mitotic kinesin, has been shown to play a role in maintaining bipolar spindle integrity and promotes viability of CIN cancer cells. To explore the potential of KIF18A, a series of inhibitors was identified. Optimization of an initial hit led to the discovery of analogues that could be used as chemical probes to interrogate the role of KIF18A inhibition. Compounds 23 and 24 caused significant mitotic arrest in vivo, which was sustained for 24 h. This would be followed by cell death either in mitosis or in the subsequent interphase. Furthermore, photoaffinity labeling experiments reveal that this series of inhibitors binds at the interface of KIF18A and tubulin. This study represents the first disclosure of KIF18A inhibitors with in vivo activity.
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Affiliation(s)
- Nuria A Tamayo
- Medicinal Chemistry, Amgen Research, One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Matthew P Bourbeau
- Medicinal Chemistry, Amgen Research, One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Jennifer R Allen
- Medicinal Chemistry, Amgen Research, One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Kate S Ashton
- Medicinal Chemistry, Amgen Research, One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Jian Jeffrey Chen
- Medicinal Chemistry, Amgen Research, One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Matthew R Kaller
- Medicinal Chemistry, Amgen Research, One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Thomas T Nguyen
- Medicinal Chemistry, Amgen Research, One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Nobuko Nishimura
- Medicinal Chemistry, Amgen Research, One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Liping H Pettus
- Medicinal Chemistry, Amgen Research, One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Mary Walton
- Medicinal Chemistry, Amgen Research, One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Brian Belmontes
- Oncology Research, Amgen Research, One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Jodi Moriguchi
- Oncology Research, Amgen Research, One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Kui Chen
- Discovery Technologies, Amgen Research, One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - John D McCarter
- Discovery Technologies, Amgen Research, One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Kelly Hanestad
- Oncology Research, Amgen Research, One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Grace Chung
- Oncology Research, Amgen Research, One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Maria Stefania S Ninniri
- Oncology Research, Amgen Research, One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Jan Sun
- Oncology Research, Amgen Research, One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Leszek Poppe
- Discovery Attribute Sciences, Amgen Research, One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Chris Spahr
- Discovery Attribute Sciences, Amgen Research, One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - John Hui
- Discovery Attribute Sciences, Amgen Research, One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Lei Jia
- Computational & Data Sciences, Amgen Research, One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Tian Wu
- Pre-Pivotal Drug Product, Amgen Research, One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Upendra P Dahal
- Pharmacokinetics and Drug Metabolism, Amgen Research, 1120 Veterans Blvd., South San Francisco, California 94080, United States
| | - Katheryne Z Edson
- Pharmacokinetics and Drug Metabolism, Amgen Research, One Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Marc Payton
- Oncology Research, Amgen Research, One Amgen Center Drive, Thousand Oaks, California 91320, United States
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8
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Farooq S, Ngaini Z. One‐pot
and
two‐pot
methods for chalcone derived pyrimidines synthesis and applications. J Heterocycl Chem 2021. [DOI: 10.1002/jhet.4226] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Saba Farooq
- Faculty of Resource Science and Technology Universiti Malaysia Sarawak Kota Samarahan Malaysia
| | - Zainab Ngaini
- Faculty of Resource Science and Technology Universiti Malaysia Sarawak Kota Samarahan Malaysia
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9
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Villari G, Enrico Bena C, Del Giudice M, Gioelli N, Sandri C, Camillo C, Fiorio Pla A, Bosia C, Serini G. Distinct retrograde microtubule motor sets drive early and late endosome transport. EMBO J 2020; 39:e103661. [PMID: 33215754 PMCID: PMC7737607 DOI: 10.15252/embj.2019103661|] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Although subcellular positioning of endosomes significantly impacts on their functions, the molecular mechanisms governing the different steady-state distribution of early endosomes (EEs) and late endosomes (LEs)/lysosomes (LYs) in peripheral and perinuclear eukaryotic cell areas, respectively, are still unsolved. We unveil that such differences arise because, while LE retrograde transport depends on the dynein microtubule (MT) motor only, the one of EEs requires the cooperative antagonism of dynein and kinesin-14 KIFC1, a MT minus end-directed motor involved in cancer progression. Mechanistically, the Ser-x-Ile-Pro (SxIP) motif-mediated interaction of the endoplasmic reticulum transmembrane protein stromal interaction molecule 1 (STIM1) with the MT plus end-binding protein 1 (EB1) promotes its association with the p150Glued subunit of the dynein activator complex dynactin and the distinct location of EEs and LEs/LYs. The peripheral distribution of EEs requires their p150Glued-mediated simultaneous engagement with dynein and SxIP motif-containing KIFC1, via HOOK1 and HOOK3 adaptors, respectively. In sum, we provide evidence that distinct minus end-directed MT motor systems drive the differential transport and subcellular distribution of EEs and LEs in mammalian cells.
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Affiliation(s)
- Giulia Villari
- Department of OncologyUniversity of Torino School of MedicineCandioloItaly,Candiolo Cancer Institute ‐ Fondazione del Piemonte per l'Oncologia (FPO)Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS)TorinoItaly
| | - Chiara Enrico Bena
- Candiolo Cancer Institute ‐ Fondazione del Piemonte per l'Oncologia (FPO)Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS)TorinoItaly,IIGM ‐ Italian Institute for Genomic MedicineCandioloItaly,Present address:
Sorbonne UniversitéCNRS, Institut de Biologie Paris‐SeineLaboratoire Jean Perrin (LJP)ParisFrance
| | - Marco Del Giudice
- Candiolo Cancer Institute ‐ Fondazione del Piemonte per l'Oncologia (FPO)Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS)TorinoItaly,IIGM ‐ Italian Institute for Genomic MedicineCandioloItaly
| | - Noemi Gioelli
- Department of OncologyUniversity of Torino School of MedicineCandioloItaly,Candiolo Cancer Institute ‐ Fondazione del Piemonte per l'Oncologia (FPO)Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS)TorinoItaly
| | - Chiara Sandri
- Department of OncologyUniversity of Torino School of MedicineCandioloItaly,Candiolo Cancer Institute ‐ Fondazione del Piemonte per l'Oncologia (FPO)Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS)TorinoItaly
| | - Chiara Camillo
- Department of OncologyUniversity of Torino School of MedicineCandioloItaly,Candiolo Cancer Institute ‐ Fondazione del Piemonte per l'Oncologia (FPO)Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS)TorinoItaly
| | | | - Carla Bosia
- IIGM ‐ Italian Institute for Genomic MedicineCandioloItaly,Department of Applied Science and TechnologyPolytechnic of TorinoTorinoItaly
| | - Guido Serini
- Department of OncologyUniversity of Torino School of MedicineCandioloItaly,Candiolo Cancer Institute ‐ Fondazione del Piemonte per l'Oncologia (FPO)Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS)TorinoItaly
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10
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Villari G, Enrico Bena C, Del Giudice M, Gioelli N, Sandri C, Camillo C, Fiorio Pla A, Bosia C, Serini G. Distinct retrograde microtubule motor sets drive early and late endosome transport. EMBO J 2020; 39:e103661. [PMID: 33215754 PMCID: PMC7737607 DOI: 10.15252/embj.2019103661] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 10/01/2020] [Accepted: 10/14/2020] [Indexed: 11/23/2022] Open
Abstract
Although subcellular positioning of endosomes significantly impacts on their functions, the molecular mechanisms governing the different steady‐state distribution of early endosomes (EEs) and late endosomes (LEs)/lysosomes (LYs) in peripheral and perinuclear eukaryotic cell areas, respectively, are still unsolved. We unveil that such differences arise because, while LE retrograde transport depends on the dynein microtubule (MT) motor only, the one of EEs requires the cooperative antagonism of dynein and kinesin‐14 KIFC1, a MT minus end‐directed motor involved in cancer progression. Mechanistically, the Ser‐x‐Ile‐Pro (SxIP) motif‐mediated interaction of the endoplasmic reticulum transmembrane protein stromal interaction molecule 1 (STIM1) with the MT plus end‐binding protein 1 (EB1) promotes its association with the p150Glued subunit of the dynein activator complex dynactin and the distinct location of EEs and LEs/LYs. The peripheral distribution of EEs requires their p150Glued‐mediated simultaneous engagement with dynein and SxIP motif‐containing KIFC1, via HOOK1 and HOOK3 adaptors, respectively. In sum, we provide evidence that distinct minus end‐directed MT motor systems drive the differential transport and subcellular distribution of EEs and LEs in mammalian cells.
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Affiliation(s)
- Giulia Villari
- Department of Oncology, University of Torino School of Medicine, Candiolo, Italy.,Candiolo Cancer Institute - Fondazione del Piemonte per l'Oncologia (FPO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Torino, Italy
| | - Chiara Enrico Bena
- Candiolo Cancer Institute - Fondazione del Piemonte per l'Oncologia (FPO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Torino, Italy.,IIGM - Italian Institute for Genomic Medicine, Candiolo, Italy
| | - Marco Del Giudice
- Candiolo Cancer Institute - Fondazione del Piemonte per l'Oncologia (FPO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Torino, Italy.,IIGM - Italian Institute for Genomic Medicine, Candiolo, Italy
| | - Noemi Gioelli
- Department of Oncology, University of Torino School of Medicine, Candiolo, Italy.,Candiolo Cancer Institute - Fondazione del Piemonte per l'Oncologia (FPO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Torino, Italy
| | - Chiara Sandri
- Department of Oncology, University of Torino School of Medicine, Candiolo, Italy.,Candiolo Cancer Institute - Fondazione del Piemonte per l'Oncologia (FPO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Torino, Italy
| | - Chiara Camillo
- Department of Oncology, University of Torino School of Medicine, Candiolo, Italy.,Candiolo Cancer Institute - Fondazione del Piemonte per l'Oncologia (FPO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Torino, Italy
| | - Alessandra Fiorio Pla
- Department of Life Sciences and Systems Biology, University of Torino, Torino, Italy
| | - Carla Bosia
- IIGM - Italian Institute for Genomic Medicine, Candiolo, Italy.,Department of Applied Science and Technology, Polytechnic of Torino, Torino, Italy
| | - Guido Serini
- Department of Oncology, University of Torino School of Medicine, Candiolo, Italy.,Candiolo Cancer Institute - Fondazione del Piemonte per l'Oncologia (FPO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Torino, Italy
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11
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Łomzik M, Hanif M, Budniok A, Błauż A, Makal A, Tchoń DM, Leśniewska B, Tong KKH, Movassaghi S, Söhnel T, Jamieson SMF, Zafar A, Reynisson J, Rychlik B, Hartinger CG, Plażuk D. Metal-Dependent Cytotoxic and Kinesin Spindle Protein Inhibitory Activity of Ru, Os, Rh, and Ir Half-Sandwich Complexes of Ispinesib-Derived Ligands. Inorg Chem 2020; 59:14879-14890. [PMID: 33003697 PMCID: PMC7584371 DOI: 10.1021/acs.inorgchem.0c00957] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Ispinesib is a potent inhibitor of kinesin spindle protein (KSP), which has been identified as a promising target for antimitotic anticancer drugs. Herein, we report the synthesis of half-sandwich complexes of Ru, Os, Rh, and Ir bearing the ispinesib-derived N,N-bidentate ligands (R)- and (S)-2-(1-amino-2-methylpropyl)-3-benzyl-7-chloroquinazolin-4(3H)-one and studies on their chemical and biological properties. Using the enantiomerically pure (R)- and (S)-forms of the ligand, depending on the organometallic moiety, either the SM,R or RM,S diastereomers, respectively, were observed in the molecular structures of the Ru- and Os(cym) (cym = η6-p-cymene) compounds, whereas the RM,R or SM,S diastereomers were found for the Rh- and Ir(Cp*) (Cp* = η5-pentamethylcyclopentadienyl) derivatives. However, density functional theory (DFT) calculations suggest that the energy difference between the diastereomers is very small, and therefore a mixture of both will be present in solution. The organometallics exhibited varying antiproliferative activity in a series of human cancer cell lines, with the complexes featuring the (R)-enantiomer of the ligand being more potent than the (S)-configured counterparts. Notably, the Rh and Ir complexes demonstrated high KSP inhibitory activity, even at 1 nM concentration, which was independent of the chirality of the ligand, whereas the Ru and especially the Os derivatives were much less active.
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Affiliation(s)
- Michał Łomzik
- Department of Organic Chemistry, Faculty of Chemistry, University of Łódź, ul. Tamka 12, 91-403 Łódź, Poland
| | - Muhammad Hanif
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Aleksandra Budniok
- Cytometry Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Łódź, ul. Pomorska 141/143, 90-236 Łódź, Poland
| | - Andrzej Błauż
- Cytometry Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Łódź, ul. Pomorska 141/143, 90-236 Łódź, Poland
| | - Anna Makal
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, ul. Żwirki i Wigury 101, 02-089 Warszawa, Poland
| | - Daniel M Tchoń
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, ul. Żwirki i Wigury 101, 02-089 Warszawa, Poland
| | - Barbara Leśniewska
- Faculty of Chemistry, University of Białystok, ul. K. Ciołkowskiego 1 K, 15-245 Białystok, Poland
| | - Kelvin K H Tong
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Sanam Movassaghi
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Tilo Söhnel
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Stephen M F Jamieson
- Auckland Cancer Society Research Centre, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Ayesha Zafar
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Jóhannes Reynisson
- School of Pharmacy and Bioengineering, Keele University, Hornbeam Building, Staffordshire ST5 5BG, United Kingdom
| | - Błażej Rychlik
- Cytometry Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Łódź, ul. Pomorska 141/143, 90-236 Łódź, Poland
| | - Christian G Hartinger
- School of Chemical Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Damian Plażuk
- Department of Organic Chemistry, Faculty of Chemistry, University of Łódź, ul. Tamka 12, 91-403 Łódź, Poland
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12
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Ranjan Dwivedi A, Kumar V, Kaur H, Kumar N, Prakash Yadav R, Poduri R, Baranwal S, Kumar V. Anti-proliferative potential of triphenyl substituted pyrimidines against MDA-MB-231, HCT-116 and HT-29 cancer cell lines. Bioorg Med Chem Lett 2020; 30:127468. [PMID: 32768647 DOI: 10.1016/j.bmcl.2020.127468] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 07/26/2020] [Accepted: 08/03/2020] [Indexed: 12/17/2022]
Abstract
A series of triphenyl substituted pyrimidines as analogous of colchicine and combretastatin A-4 was synthesized and evaluated for the antiproliferative potential. The compounds were screened against MDA-MB-231, HCT-116 and HT-29 cell lines using MTT assay. Most of the compounds displayed antiproliferative activity in low to sub micro molar concentration. Amongst the synthesized derivatives, compounds HK-2, HK-10 and HK-13 were found to be effective against all the three cancer cell lines. HK-2 exhibited IC50 values of 3.39 µM, 4.78 µM and 4.23 µM, HK-10 showed IC50 values of 0.81 µM, 5.89 µM, 4.96 µM and HK-13 showed IC50 values 3.24 µM, 4.93 µM and 4.73 µM against MDA-MB-231, HCT-116 and HT-29 cancer cell lines, respectively. HK-10 was found to be the most potent compound in the series with IC50 values of 0.81 µM against MDA-MB-231. In the cell cycle analysis, HK-2 and HK-10 showed cell arrest at G2/M phase of the cell cycle while HK-13 inhibited cell growth at the G1/G0 phase. All the three compounds showed cell death induced through apoptosis. In the docking studies, HK-2, HK-10 and HK-13 were found to fit well in the colchicine binding site of the tubulin. Some of the compounds in the current series were found to be promising against all the three cancer cell lines and may act as potent leads for further development.
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Affiliation(s)
- Ashish Ranjan Dwivedi
- Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Bathinda, Punjab 151001, India
| | - Vijay Kumar
- Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Bathinda, Punjab 151001, India
| | - Harmeet Kaur
- Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Bathinda, Punjab 151001, India
| | - Naveen Kumar
- Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Bathinda, Punjab 151001, India
| | - Ravi Prakash Yadav
- Department of Microbiology, School of Basic and Applied Sciences, Central University of Punjab, Bathinda, Punjab 151001, India
| | - Ramarao Poduri
- Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Bathinda, Punjab 151001, India
| | - Somesh Baranwal
- Department of Microbiology, School of Basic and Applied Sciences, Central University of Punjab, Bathinda, Punjab 151001, India.
| | - Vinod Kumar
- Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Bathinda, Punjab 151001, India; Laboratory of Organic and Medicinal Chemistry, Department of Chemistry, Central University of Punjab, Bathinda, Punjab 151001, India.
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13
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Inhibition of kinesin motor protein KIFC1 by AZ82 induces multipolar mitosis and apoptosis in prostate cancer cell. Gene 2020; 760:144989. [PMID: 32717307 DOI: 10.1016/j.gene.2020.144989] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 06/28/2020] [Accepted: 07/21/2020] [Indexed: 12/14/2022]
Abstract
Kinesin 14 family member KIFC1 is a mitotic kinesin which contains a C-terminal motor domain and plays a vital role for clustering the amplified centrosomes. Overexpression of KIFC1 in prostate cancer (PCa) cells showed resistance to docetaxel (DTX). The present study revealed that small KIFC1 inhibitor AZ82 suppresed the transcription and translation of KIFC1 significantly in PCa cells. AZ82 inhibited the KIFC1 expression both in the cytoplasm and nucleus of PCa cells. Inhibition of KIFC1 by AZ82 caused multipolar mitosis in PCa cells via de-clustering the amplified centrosomes and decreased the rate of cancer cell growth and proliferation. Moreover, depletion of KIFC1 reduced cells entering the cell cycle and caused PCa cells death through apoptosis by increasing the expression of Bax and Cytochrome C. Thereby, KIFC1 silencing and inhibition decreased the PCa cells survival by inducing multipolar mitosis as well as apoptosis, suggesting inhibition of KIFC1 using AZ82 might be a strategy to treat PCa by controlling the cancer cell proliferation.
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14
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Joshi T, Joshi T, Sharma P, Pundir H, Chandra S. In silico identification of natural fungicide from Melia azedarach against isocitrate lyase of Fusarium graminearum. J Biomol Struct Dyn 2020; 39:4816-4834. [PMID: 32568603 DOI: 10.1080/07391102.2020.1780941] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Isocitrate Lyase (ICL) is a crucial enzyme involved in the Glyoxylate pathway, essential for the virulence of several fungal pathogens including Fusarium graminearum. ICL is a novel target for the discovery of antifungal compounds and F. graminearum ICL inhibitors can be used to control the growth of this fungus. Although, several inhibitors of ICL have been identified, however, most of these inhibitors are not environment-friendly. Hence there is still a need to discover natural inhibitors of ICL that can be more effective. To identify a potential antifungal compound, we performed a structure-based screening of phytochemicals of Melia azedarach against the FgICL structure by molecular docking and 104 ligands were found to have a better docking score as compared to the reference molecule. These compounds were assessed for drug-likeness and ADMET prediction. After molecular docking, drug-likeness and toxicity analysis, six potential compounds (Melianoninol (-6.6 kcal/mol), Nimbinene (-7.7 kcal/mol), Vilasinin (-8.1 kcal/mol), Fraxinellone (-6.7 kcal/mol), Gedunin (-7.8 kcal/mol), and Meldenin (-7.8 kcal/mol)) were subjected for rescoring by X-Score. The structural stability and dynamics of screened compounds at the active site of FgICL were examined using MD simulation and MM-PBSA analysis. The result of MM-PBSA revealed that four phytochemicals viz. Melianoninol, Nimbinene, Vilasinin, and Fraxinellone had binding free energy of -17.25 kcal/mol, -59.35 kcal/mol, -64.79 kcal/mol, and -29.86 kcal/mol, respectively. Molecular dynamics simulation and MM-PBSA demonstrated that these four phytochemicals displayed considerable significant structural and pharmacological properties and could be probable antifungal drug candidates against F. graminearum. These phyotchemicals of M. azedarach may be suitable candidates for further experimental analysis. [Formula: see text]Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Tanuja Joshi
- Department of Botany, Kumaun University, Almora, Uttarakhand, India
| | - Tushar Joshi
- Department of Botany, Kumaun University, Almora, Uttarakhand, India.,Department of Biotechnology, Bhimtal Campus, Kumaun University, Nainital, Uttarakhand, India
| | - Priyanka Sharma
- Department of Botany, Kumaun University, Nainital, Uttarakhand, India
| | - Hemlata Pundir
- Department of Botany, Kumaun University, Nainital, Uttarakhand, India
| | - Subhash Chandra
- Department of Botany, Kumaun University, Almora, Uttarakhand, India
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15
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Joshi T, Joshi T, Sharma P, Chandra S, Pande V. Molecular docking and molecular dynamics simulation approach to screen natural compounds for inhibition of Xanthomonas oryzae pv. Oryzae by targeting peptide deformylase. J Biomol Struct Dyn 2020; 39:823-840. [PMID: 31965918 DOI: 10.1080/07391102.2020.1719200] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Xanthomonas oryzae pv. Oryzae (Xoo) causes bacterial leaf blight (BLB) of rice which results in a huge loss in production. Many chemicals are used to control BLB disease. However, these chemicals are toxic to the environments, animals and human beings. Thus, there is a demand to discover potential and safe natural pesticides to manage BLB disease successfully. Therefore, we screened a library of phytochemicals of different plants having antibacterial activity by targeting Peptide Deformylase (PDF) of Xoo using in silico techniques. A library of 318 phytochemicals was prepared and subjected to rigid and flexible molecular docking against PDF followed by molecular dynamics simulation and free energy analysis of protein-ligand complexes. The results of virtual screening showed that 14 compounds from different plants have good binding energy as compare to reference molecule (3 R)-2,3-dihydro[1,3] thiazolo [3,2 a]benzimidazol-3-ol) (-7.7 kcal mol-1). Out of 14 hit compounds, eight compounds that were selected based on binding energy were analyzed by Molecular dynamic (MD) simulation. Analysis of MD simulation revealed that eight compounds namely; Bisdemethoxycurcumin, Rosmarinic acid, Piperanine, Dihydropiperlonguminine, Piperdardine, Dihydrocurcumin and Lonhumosides B achieved good stability during the 80 ns MD simulation at 300 K in term of the RMSD. Further, we calculated RMSF, RG, SASA, and interaction energy after 40 ns due to showing the stability of complexes. From our results, we conclude that these natural compounds could inhibit Xoo by targeting PDF receptor and can be used as potential bactericidal candidates against BLB disease of rice against Xoo and other bacteria. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Tushar Joshi
- Department of Biotechnology, Kumaun University, Bhimtal, Uttarakhand, India.,Department of Botany, Kumaun University, Almora, Uttarakhand, India
| | - Tanuja Joshi
- Department of Botany, Kumaun University, Almora, Uttarakhand, India
| | - Priyanka Sharma
- Department of Botany, Kumaun University, Nainital, Uttarakhand, India
| | - Subhash Chandra
- Department of Botany, Kumaun University, Almora, Uttarakhand, India
| | - Veena Pande
- Department of Biotechnology, Kumaun University, Bhimtal, Uttarakhand, India
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16
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Hao SL, Yang WX. KIFC1 is essential for normal spermatogenesis and its depletion results in early germ cell apoptosis in the Kuruma shrimp, Penaeus (Marsupenaeus) japonicus. Aging (Albany NY) 2019; 11:12773-12792. [PMID: 31895691 PMCID: PMC6949060 DOI: 10.18632/aging.102601] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 12/02/2019] [Indexed: 12/24/2022]
Abstract
In order to explore the dynamic mechanisms during spermatogenesis of the penaeid prawns, the full length of kifc1 was cloned from testis cDNA of Penaeus japonicus through RACE. Both semi-quantitative RT-PCR and Western blot results indicated that KIFC1 was extensive expressed in different tissue of P. japonicus. Compared with other tissue, the highest expression of KIFC1 occurred in the testis. According to the immunofluorescence results, the KIFC1 protein was detected at each stage of whole process of spermatogenesis. In the spermatogonial phase, KIFC1 mainly dispersed in cytoplasm and co-localized with microtubules, while abundant KIFC1 signal was detected in the nucleus of spermatocytes. At the early stage of spermatids, KIFC1 was transported from the nucleus into the cytoplasm, and it assisted microtubule assembly onto one side of the nucleus. Finally, in mature sperm, it was weakly expressed in the acrosome. This implies that KIFC1 may participate in the mitosis of spermatogonia, meiosis of spermatocyte, and acrosome formation during spermiogenesis; it may also play functions in acrosome maintaining in mature sperm. In addition, the results of KIFC1 knockdown by dsRNA injection in vivo reveal that decreased KIFC1 expression may induce aberrant microtubule assembly, and it leads to spermatogonia and spermatocyte apoptosis.
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Affiliation(s)
- Shuang-Li Hao
- The Sperm Laboratory, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Wan-Xi Yang
- The Sperm Laboratory, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
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17
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Interactions between motor domains in kinesin-14 Ncd - a molecular dynamics study. Biochem J 2019; 476:2449-2462. [PMID: 31416830 DOI: 10.1042/bcj20190484] [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: 06/24/2019] [Revised: 08/11/2019] [Accepted: 08/15/2019] [Indexed: 11/17/2022]
Abstract
Minus-end directed, non-processive kinesin-14 Ncd is a dimeric protein with C-terminally located motor domains (heads). Generation of the power-stroke by Ncd consists of a lever-like rotation of a long superhelical 'stalk' segment while one of the kinesin's heads is bound to the microtubule. The last ∼30 amino acids of Ncd head play a crucial but still poorly understood role in this process. Here, we used accelerated molecular dynamics simulations to explore the conformational dynamics of several systems built upon two crystal structures of Ncd, the asymmetrical T436S mutant in pre-stroke/post-stroke conformations of two partner subunits and the symmetrical wild-type protein in pre-stroke conformation of both subunits. The results revealed a new conformational state forming following the inward motion of the subunits and stabilized with several hydrogen bonds to residues located on the border or within the C-terminal linker, i.e. a modeled extension of the C-terminus by residues 675-683. Forming of this new, compact Ncd conformation critically depends on the length of the C-terminus extending to at least residue 681. Moreover, the associative motion leading to the compact conformation is accompanied by a partial lateral rotation of the stalk. We propose that the stable compact conformation of Ncd may represent an initial state of the working stroke.
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18
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Saini G, Dalal V, Savita BK, Sharma N, Kumar P, Sharma AK. Molecular docking and dynamic approach to virtual screen inhibitors against Esbp of Candidatus Liberibacter asiaticus. J Mol Graph Model 2019; 92:329-340. [PMID: 31446203 DOI: 10.1016/j.jmgm.2019.08.012] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 07/29/2019] [Accepted: 08/15/2019] [Indexed: 12/21/2022]
Abstract
Citrus greening (huanglongbing) is the most destructive disease of citrus worldwide caused by Candidatus Liberibacter asiaticus (CLA). Currently, no strategies have been developed to manage the Huanglongbing (HLB) disease and to stop the spreading of this disease to new citrus areas. Esbp is an extracellular solute-binding protein, involved in the uptake of iron in CLA. Thus, inhibiting this process may be a promising approach to design a drug against CLA. Thus, the present study focused on the identification of novel effective inhibitors which can inhibit the activity of CLas Esbp. A series of small molecules were screened against the CLas Esbp and the binding affinities were assessed using docking simulation studies. Top scored molecules were screened for different pharmacophore properties and Inhibitory Concentration 50 (IC50) values. Density functional theory was employed to check the chemical properties of the molecules. Further, Molecular Dynamics simulation analysis like RMSD, RMSF, Rg, SASA and MMPBSA results reveal that the identified molecules (ZINC03143779, ZINC05491830, ZINC19210425, ZINC08750867, and ZINC14671545) exhibit a good binding affinity for CLas Esbp and results in the formation of stable CLas Esbp-inhibitor(s) complex. The present study reported that these compounds appeared to be the suitable novel inhibitor of CLas Esbp and pave the way to further development of antimicrobial agents against CLA.
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Affiliation(s)
- Gunjan Saini
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, 247 667, India
| | - Vikram Dalal
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, 247 667, India
| | - Brajesh Kumar Savita
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, 247 667, India
| | - Nidhi Sharma
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, 247 667, India
| | - Pravindra Kumar
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, 247 667, India
| | - Ashwani Kumar Sharma
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, 247 667, India.
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19
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Shuaib S, Narang SS, Goyal D, Goyal B. Computational design and evaluation of β‐sheet breaker peptides for destabilizing Alzheimer's amyloid‐β
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protofibrils. J Cell Biochem 2019; 120:17935-17950. [DOI: 10.1002/jcb.29061] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Revised: 04/20/2019] [Accepted: 04/29/2019] [Indexed: 12/19/2022]
Affiliation(s)
- Suniba Shuaib
- Department of Chemistry, Faculty of Basic and Applied Sciences Sri Guru Granth Sahib World University Fatehgarh Sahib India
| | - Simranjeet Singh Narang
- Department of Chemistry, Faculty of Basic and Applied Sciences Sri Guru Granth Sahib World University Fatehgarh Sahib India
| | - Deepti Goyal
- Department of Chemistry, Faculty of Basic and Applied Sciences Sri Guru Granth Sahib World University Fatehgarh Sahib India
| | - Bhupesh Goyal
- School of Chemistry & Biochemistry Thapar Institute of Engineering & Technology Patiala India
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20
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Taglieri L, Saccoliti F, Nicolai A, Peruzzi G, Madia VN, Tudino V, Messore A, Di Santo R, Artico M, Taurone S, Salvati M, Costi R, Scarpa S. Discovery of a pyrimidine compound endowed with antitumor activity. Invest New Drugs 2019; 38:39-49. [PMID: 30900116 DOI: 10.1007/s10637-019-00762-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 03/08/2019] [Indexed: 02/07/2023]
Abstract
Recently, some synthetic nitrogen-based heterocyclic molecules, such as PJ34, have shown pronounced antitumor activity. Therefore, we designed and synthesized new derivatives characterized by a nitrogen-containing scaffold and evaluated their antiproliferative properties in tumor cells. We herein report the effects of three newly synthesized compounds on cell lines from three different human cancers: triple-negative breast cancer, colon carcinoma and glioblastoma. We found that two of these compounds did not affect proliferation, while the third significantly inhibited replication of the three cell lines. Moreover, this third molecule at 20 μM led to the upregulation of p21 and p27 and blockage of the cell cycle at G0/G1; in addition, it induced apoptosis in all three cell lines when used at higher concentrations (30-50 μM). The results demonstrate that this compound is a potent inhibitor of replication, an inducer of apoptosis and a negative regulator of cell cycle progression for cancer cells of different histotypes. Our data suggest a potential role for this new molecule as an interesting and powerful tool for new approaches in treating various cancers.
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Affiliation(s)
- Ludovica Taglieri
- Department of Experimental Medicine, Sapienza University, Viale Regina Elena 324, 00161, Rome, Italy
| | - Francesco Saccoliti
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza University, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Alice Nicolai
- Department of Experimental Medicine, Sapienza University, Viale Regina Elena 324, 00161, Rome, Italy
- Department of Sensory Organs, Sapienza University, Viale del Policlinico 155, 00161, Rome, Italy
| | - Giovanna Peruzzi
- Italian Institute of Technology, Center for Life Nanoscience@Sapienza, Viale Regina Elena 324, 00161, Rome, Italy
| | - Valentina Noemi Madia
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza University, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Valeria Tudino
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza University, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Antonella Messore
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza University, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Roberto Di Santo
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza University, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Marco Artico
- Department of Sensory Organs, Sapienza University, Viale del Policlinico 155, 00161, Rome, Italy
| | - Samanta Taurone
- Department of Sensory Organs, Sapienza University, Viale del Policlinico 155, 00161, Rome, Italy
| | - Maurizio Salvati
- Department of Human Neurosciences, Sapienza University, Viale Regina Elena 324, 00161, Rome, Italy
| | - Roberta Costi
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza University, Piazzale Aldo Moro 5, 00185, Rome, Italy.
| | - Susanna Scarpa
- Department of Experimental Medicine, Sapienza University, Viale Regina Elena 324, 00161, Rome, Italy
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Mitotic Motor KIFC1 Is an Organizer of Microtubules in the Axon. J Neurosci 2019; 39:3792-3811. [PMID: 30804089 DOI: 10.1523/jneurosci.3099-18.2019] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 01/30/2019] [Accepted: 02/18/2019] [Indexed: 11/21/2022] Open
Abstract
KIFC1 (also called HSET or kinesin-14a) is best known as a multifunctional motor protein essential for mitosis. The present studies are the first to explore KIFC1 in terminally postmitotic neurons. Using RNA interference to partially deplete KIFC1 from rat neurons (from animals of either gender) in culture, pharmacologic agents that inhibit KIFC1, and expression of mutant KIFC1 constructs, we demonstrate critical roles for KIFC1 in regulating axonal growth and retraction as well as growth cone morphology. Experimental manipulations of KIFC1 elicit morphological changes in the axon as well as changes in the organization, distribution, and polarity orientation of its microtubules. Together, the results indicate a mechanism by which KIFC1 binds to microtubules in the axon and slides them into alignment in an ATP-dependent fashion and then cross-links them in an ATP-independent fashion to oppose their subsequent sliding by other motors.SIGNIFICANCE STATEMENT Here, we establish that KIFC1, a molecular motor well characterized in mitosis, is robustly expressed in neurons, where it has profound influence on the organization of microtubules in a number of different functional contexts. KIFC1 may help answer long-standing questions in cellular neuroscience such as, mechanistically, how growth cones stall and how axonal microtubules resist forces that would otherwise cause the axon to retract. Knowledge about KIFC1 may help researchers to devise strategies for treating disorders of the nervous system involving axonal retraction given that KIFC1 is expressed in adult neurons as well as developing neurons.
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Sherin L, Farwa S, Sohail A, Li Z, Bég OA. Cancer drug therapy and stochastic modeling of "nano-motors". Int J Nanomedicine 2018; 13:6429-6440. [PMID: 30410329 PMCID: PMC6198871 DOI: 10.2147/ijn.s168780] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Background Controlled inhibition of kinesin motor proteins is highly desired in the field of oncology. Among other interventions, there exists “targeted chemotherapeutic regime/options” of selective Eg5 competitive and allosteric inhibitors, inducing cancer cell apoptosis and tumor regression with improved safety profiles. Research question Though promising, such studies are still under clinical trials, for the discovery of efficient and least harmful Eg5 inhibitors. The aim of this research was to bridge the computational modeling approach with drug design and therapy of cancer cells. Methods A computational model, interfaced with the clinical data of “Eg5 dynamics” and “inhibitors” via special functions, is presented in this article. Comparisons are made for the drug efficacy, and the threshold values are predicted through numerical simulations. Results Results are obtained to depict the dynamics induced by ispinesib, when used as an inhibitor of kinesin Eg5, on cancer cell lines.
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Affiliation(s)
- Lubna Sherin
- Department of Chemistry, COMSATS University Islamabad, Lahore 54000, Pakistan
| | - Shabieh Farwa
- Department of Mathematics, COMSATS University Islamabad, Wah Cantt, Pakistan
| | - Ayesha Sohail
- Department of Mathematics, COMSATS University Islamabad, Lahore 54000, Pakistan,
| | - Zhiwu Li
- Institute of Systems Engineering, Macau University of Science and Technology, Taipa, Macau.,School of Electro-Mechanical Engineering, Xidian University, Xi'an 710071, China
| | - O Anwar Bég
- Fluid Mechanics, Spray Research Group, Mechanical and Petroleum Engineering, School of Computing, Science and Engineering, G77, University of Salford, Manchester M54WT, UK
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Yukawa M, Yamauchi T, Kurisawa N, Ahmed S, Kimura KI, Toda T. Fission yeast cells overproducing HSET/KIFC1 provides a useful tool for identification and evaluation of human kinesin-14 inhibitors. Fungal Genet Biol 2018; 116:33-41. [DOI: 10.1016/j.fgb.2018.04.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 03/29/2018] [Accepted: 04/07/2018] [Indexed: 12/14/2022]
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Sadakane K, Alrazi IMD, Maruta S. Highly efficient photocontrol of mitotic kinesin Eg5 ATPase activity using a novel photochromic compound composed of two azobenzene derivatives. J Biochem 2018; 164:295-301. [DOI: 10.1093/jb/mvy051] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 05/20/2018] [Indexed: 11/14/2022] Open
Affiliation(s)
- Kei Sadakane
- Department of Bioinformatics, Graduate School of Engineering Soka University, 1-236 Tangi-cho, Hachioji, Tokyo, Japan
| | - Islam M D Alrazi
- Department of Bioinformatics, Graduate School of Engineering Soka University, 1-236 Tangi-cho, Hachioji, Tokyo, Japan
| | - Shinsaku Maruta
- Department of Bioinformatics, Graduate School of Engineering Soka University, 1-236 Tangi-cho, Hachioji, Tokyo, Japan
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