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Liu Y, Deng L, Ding F, Wang Q, Zhang S, Mi N, Zhang W, Zeng B, Tong H, Wu L. Discovery of novel cholesteryl ester transfer protein (CETP) inhibitors by a multi-stage virtual screening. BMC Chem 2024; 18:95. [PMID: 38702788 PMCID: PMC11069292 DOI: 10.1186/s13065-024-01192-5] [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: 02/03/2024] [Accepted: 04/17/2024] [Indexed: 05/06/2024] Open
Abstract
Cholesteryl ester transfer protein (CETP) is a promising therapeutic target for cardiovascular diseases. It effectively lowers the low-density lipoprotein cholesterol levels and increases the high-density lipoprotein cholesterol levels in the human plasma. This study identified novel and highly potent CETP inhibitors using virtual screening techniques. Molecular docking and molecular dynamics (MD) simulations revealed the binding patterns of these inhibitors, with the top 50 compounds selected according to their predicted binding affinity. Protein-ligand interaction analyses were performed, leading to the selection of 26 compounds for further evaluation. A CETP inhibition assay confirmed the inhibitory activities of the selected compounds. The results of the MD simulations revealed the structural stability of the protein-ligand complexes, with the binding site remaining significantly unchanged, indicating that the five compounds (AK-968/40709303, AG-690/11820117, AO-081/41378586, AK-968/12713193, and AN-465/14952302) identified have the potential as active CETP inhibitors and are promising leads for drug development.
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Affiliation(s)
- Yanfeng Liu
- Nanjing Lishui District Hospital of Traditional Chinese Medicine, Nanjing, China
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China
- School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Liangying Deng
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Feng Ding
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Qiang Wang
- Nanjing Lishui District Hospital of Traditional Chinese Medicine, Nanjing, China
| | - Shuran Zhang
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Nana Mi
- School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Wenhui Zhang
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Bailin Zeng
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Huangjin Tong
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China.
| | - Lixing Wu
- Nanjing Lishui District Hospital of Traditional Chinese Medicine, Nanjing, China.
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China.
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Al Otaibi AA, Alshammari SL, Dhahi Alsukaibi AK, Jamal A, Rajendrasozhan S, Alenezi KM, Hussain A, Khan I, Mushtaque M, Haque A. Synthesis, anticancer activity, molecular docking and molecular dynamics studies of some pyrazole-chalcone hybrids. J Biomol Struct Dyn 2024; 42:1381-1391. [PMID: 37071766 DOI: 10.1080/07391102.2023.2199867] [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: 11/09/2022] [Accepted: 03/31/2023] [Indexed: 04/20/2023]
Abstract
Four new hybrid compounds (H1-H4) bearing pyrazole (S1 and S2) and chalcone (P1 and P2) fragments were synthesized and characterized. Compounds were assayed for their ability to inhibit the proliferation of human lung (A549) and colon (Caco-2) cancer cell lines. Besides, toxicity against normal cells was determined using the human umbilical vein endothelial cells (HUVEC). In silico molecular docking, molecular dynamics (MD) simulation and absorption, distribution, metabolism, excretion, and toxicity (ADMET) studies were carried out to predict the binding modes, protein stability, drug-likeness and toxicity of the reported compounds. The in vitro anticancer activity of the tested compounds revealed dose-dependent cell-specific cytotoxicity. In silico studies revealed that the compounds have a good binding affinity, possess appropriate drug-likeness properties and have low toxicity profiles.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ahmed A Al Otaibi
- Department of Chemistry, College of Science, University of Ha'il, Ha'il, Saudi Arabia
| | - Sinad L Alshammari
- Department of Chemistry, College of Science, University of Ha'il, Ha'il, Saudi Arabia
| | | | - Azfar Jamal
- Department of Biology, College of Science, Al-Zulfi, Majmaah University, Majmaah, Riyadh Region, Saudi Arabia
- Health and Basic Science Research Centre, Majmaah University, Majmaah, Saudi Arabia
| | | | - Khalaf M Alenezi
- Department of Chemistry, College of Science, University of Ha'il, Ha'il, Saudi Arabia
| | - Afzal Hussain
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Imran Khan
- Department of Chemistry, College of Science, Sultan Qaboos University, Muscat, Oman
| | - Md Mushtaque
- Department of Chemistry, Millat College (A Constituent College of Lalit Narayan Mithila University), Darbhanga, Bihar, India
| | - Ashanul Haque
- Department of Chemistry, College of Science, University of Ha'il, Ha'il, Saudi Arabia
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Lavrentaki V, Kousaxidis A, Theodosis-Nobelos P, Papagiouvannis G, Koutsopoulos K, Nicolaou I. Design, synthesis, and pharmacological evaluation of indazole carboxamides of N-substituted pyrrole derivatives as soybean lipoxygenase inhibitors. Mol Divers 2023:10.1007/s11030-023-10775-8. [PMID: 38145424 DOI: 10.1007/s11030-023-10775-8] [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: 07/31/2023] [Accepted: 11/17/2023] [Indexed: 12/26/2023]
Abstract
In this paper, we attempted to develop a novel class of compounds against lipoxygenase, a key enzyme in the biosynthesis of leukotrienes implicated in a series of inflammatory diseases. Given the absence of appropriate human 5-lipoxygenase crystallographic data, solved soybean lipoxygenase-1 and -3 structures were used as a template to generate an accurate pharmacophore model which was further used for virtual screening purposes. Eight compounds (1-8) have been derived from the in-house library consisting of N-substituted pyrroles conjugated with 5- or 6-indazole moieties through a carboxamide linker. This study led to the discovery of hit molecule 8 bearing a naphthyl group with the IC50 value of 22 μM according to soybean lipoxygenase in vitro assay. Isosteric replacement of naphthyl ring with quinoline moieties and reduction of carbonyl carboxamide group resulted in compounds 9-12 and 13, respectively. Compound 12 demonstrated the most promising enzyme inhibition. In addition, compounds 8 and 12 were found to reduce the carrageenan-induced paw edema in vivo by 52.6 and 49.8%, respectively. In view of the encouraging outcomes concerning their notable in vitro and in vivo anti-inflammatory activities, compounds 8 and 12 could be further optimized for the discovery of novel 5-lipoxygenase inhibitors in future. A structure-based 3D pharmacophore model was used in the virtual screening of in-house library to discover novel potential 5-lipoxygenase inhibitors.
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Affiliation(s)
- Vasiliki Lavrentaki
- Department of Pharmaceutical Chemistry, School of Pharmacy, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Antonios Kousaxidis
- Department of Pharmaceutical Chemistry, School of Pharmacy, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | | | - Georgios Papagiouvannis
- Department of Pharmacy, School of Health Sciences, Frederick University, 1036, Nicosia, Cyprus
| | | | - Ioannis Nicolaou
- Department of Pharmaceutical Chemistry, School of Pharmacy, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece.
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Zothantluanga JH, Umar AK, Aswin K, Rajkhowa S, Chetia D. Revelation of potential drug targets of luteolin in Plasmodium falciparum through multi-target molecular dynamics simulation studies. J Biomol Struct Dyn 2023:1-17. [PMID: 37776013 DOI: 10.1080/07391102.2023.2263875] [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: 03/12/2023] [Accepted: 09/20/2023] [Indexed: 10/01/2023]
Abstract
In-silico techniques offer a fast, accurate, reliable, and economical approach to studying the molecular interactions between compounds and proteins. In this study, our main aim is to use in-silico techniques as a rational approach for the prediction of the molecular drug targets for luteolin against Plasmodium falciparum. Multi-target molecular docking, 100 nanoseconds (ns) molecular dynamics (MD) simulations, and Molecular Mechanics-Generalized Born Surface Area (MM-GBSA) binding free energy calculations were carried out for luteolin against dihydrofolate reductase thymidylate synthase (PfDHFR-TS), dihydroorotate dehydrogenase (PfDHODH), and falcipain-2. The native ligands of each protein were used as a reference to evaluate the performance of luteolin. Luteolin outperformed the native ligands of all proteins at molecular docking and MD simulations studies. However, in the MM-GBSA calculations, luteolin outperformed the native ligand of only PfDHFR-TS but not PfDHODH and falcipain-2. Among the studied proteins, the in-silico approach predicted PfDHFR-TS as the most favorable drug target for luteolin.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- James H Zothantluanga
- Department of Pharmaceutical Sciences, Faculty of Science and Engineering, Dibrugarh University, Dibrugarh, India
| | - Abd Kakhar Umar
- Department of Pharmaceutics and Pharmaceutical Technology, Faculty of Pharmacy, Universitas Padjadjaran, Jatinangor, Indonesia
| | - Keerthic Aswin
- Council of Scientific and Industrial Research, Institute of Genomics and Integrative Biology, New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Sanchaita Rajkhowa
- Centre for Biotechnology and Bioinformatics, Faculty of Biological Sciences, Dibrugarh University, Dibrugarh, India
| | - Dipak Chetia
- Department of Pharmaceutical Sciences, Faculty of Science and Engineering, Dibrugarh University, Dibrugarh, India
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Ghafoor NA, Kırboğa KK, Baysal Ö, Süzek BE, Silme RS. Data mining and molecular dynamics analysis to detect HIV-1 reverse transcriptase RNase H activity inhibitor. Mol Divers 2023:10.1007/s11030-023-10707-6. [PMID: 37561229 DOI: 10.1007/s11030-023-10707-6] [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: 05/30/2023] [Accepted: 07/26/2023] [Indexed: 08/11/2023]
Abstract
HIV-1 is a deadly virus that affects millions of people worldwide. In this study, we aimed to inhibit viral replication by targeting one of the HIV-1 proteins and identifying a new drug candidate. We used data mining and molecular dynamics methods on HIV-1 genomes. Based on MAUVE analysis, we selected the RNase H activity of the reverse transcriptase (R.T) enzyme as a potential target due to its low mutation rate and high conservation level. We screened about 94,000 small molecule inhibitors by virtual screening. We validated the hit compounds' stability and binding free energy through molecular dynamics simulations and MM/PBSA. Phomoarcherin B, known for its anticancer properties, emerged as the best candidate and showed potential as an HIV-1 reverse transcriptase RNase H activity inhibitor. This study presents a new target and drug candidate for HIV-1 treatment. However, in vitro and in vivo tests are required. Also, the effect of RNase H activity on viral replication and the interaction of Phomoarcherin B with other HIV-1 proteins should be investigated.
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Affiliation(s)
- Naeem Abdul Ghafoor
- Department of Molecular Biology and Genetics, Faculty of Science, Muğla Sıtkı Koçman University, Kötekli, 48121, Muğla, Turkey
| | - Kevser Kübra Kırboğa
- Bioengineering Department, Bilecik Seyh Edebali University, 11230, Bilecik, Turkey
- Informatics Institute, Istanbul Technical University, Maslak, 34469, Istanbul, Turkey
| | - Ömür Baysal
- Molecular Microbiology Unit, Department of Molecular Biology and Genetics, Faculty of Science, Muğla Sıtkı Koçman University, Kötekli, 48121, Muğla, Turkey.
| | - Barış Ethem Süzek
- Department of Computer Engineering, Faculty of Engineering, Muğla Sıtkı Koçman University, Kötekli, 48000, Muğla, Turkey
| | - Ragıp Soner Silme
- Center for Research and Practice in Biotechnology and Genetic Engineering, Istanbul University, Vezneciler, Fatih, 34119, Istanbul, Turkey
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6
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Zheng N, Jiang W, Zhang P, Ma L, Chen J, Zhang H. Repurposing of World-Approved Drugs for Potential Inhibition against Human Carbonic Anhydrase I: A Computational Study. Int J Mol Sci 2023; 24:12619. [PMID: 37628799 PMCID: PMC10454238 DOI: 10.3390/ijms241612619] [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: 07/03/2023] [Revised: 08/06/2023] [Accepted: 08/08/2023] [Indexed: 08/27/2023] Open
Abstract
Human carbonic anhydrases (hCAs) have enzymatic activities for reversible hydration of CO2 and are acknowledged as promising targets for the treatment of various diseases. Using molecular docking and molecular dynamics simulation approaches, we hit three compounds of methyl 4-chloranyl-2-(phenylsulfonyl)-5-sulfamoyl-benzoate (84Z for short), cyclothiazide, and 2,3,5,6-tetrafluoro-4-piperidin-1-ylbenzenesulfonamide (3UG for short) from the existing hCA I inhibitors and word-approved drugs. As a Zn2+-dependent metallo-enzyme, the influence of Zn2+ ion models on the stability of metal-binding sites during MD simulations was addressed as well. MM-PBSA analysis predicted a strong binding affinity of -18, -16, and -14 kcal/mol, respectively, for these compounds, and identified key protein residues for binding. The sulfonamide moiety bound to the Zn2+ ion appeared as an essential component of hCA I inhibitors. Vina software predicted a relatively large (unreasonable) Zn2+-sulfonamide distance, although the relative binding strength was reproduced with good accuracy. The selected compounds displayed potent inhibition against other hCA isoforms of II, XIII, and XIV. This work is valuable for molecular modeling of hCAs and further design of potent inhibitors.
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Affiliation(s)
| | | | | | | | | | - Haiyang Zhang
- Department of Biological Science and Engineering, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China
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Yadav S, Ahamad S, Gupta D, Mathur P. Lead optimization, pharmacophore development and scaffold design of protein kinase CK2 inhibitors as potential COVID-19 therapeutics. J Biomol Struct Dyn 2023; 41:1811-1827. [PMID: 35014595 DOI: 10.1080/07391102.2021.2024449] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Therapeutic agents being designed against COVID-19 have targeted either the virus directly or the host cellular machinery. A particularly attractive host target is the ubiquitous and constitutively active serine-threonine kinase, Protein kinase CK2 (CK2). CK2 enhances viral protein synthesis by inhibiting the sequestration of host translational machinery as stress granules and assists in viral egression via association with the N-protein at filopodial protrusions of the infected cell. CK2 inhibitors such as Silmitasertib have been proposed as possible therapeutic candidates in COVID-19 infections. The present study aims to optimize Silmitasertib, develop pharmacophore models and design unique scaffolds to modulate CK2. The lead optimization phase involved the generation of compounds structurally similar to Silmitasertib via bioisostere replacement followed by a multi-stage docking approach to identify drug-like candidates. Molecular dynamics (MD) simulations were performed for two promising candidates (ZINC-43206125 and PC-57664175) to estimate their binding stability and interaction. Top scoring candidates from the lead optimization phase were utilized to build ligand-based pharmacophore models. These models were then merged with structure-based pharmacophores (e-pharmacophores) to build a hybrid hypothesis. This hybrid hypothesis was validated against a decoy set and used to screen a diverse kinase inhibitors library to identify favored chemical features in the retrieved actives. These chemical features include; an anion, an aromatic ring and an H-bond acceptor. Based on the knowledge of these features; de-novo scaffold design was carried out which identified phenindiones, carboxylated steroids, macrocycles and peptides as novel scaffolds with the potential to modulate CK2.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Siddharth Yadav
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, Uttar Pradesh, India
| | - Shahzaib Ahamad
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Dinesh Gupta
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Puniti Mathur
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, Uttar Pradesh, India
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Ahmad S, Gupta D, Ahmed T, Islam A. Designing of new tetrahydro-β-carboline-based ABCG2 inhibitors using 3D-QSAR, molecular docking, and DFT tools. J Biomol Struct Dyn 2023; 41:14016-14027. [PMID: 36752362 DOI: 10.1080/07391102.2023.2176361] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 01/30/2023] [Indexed: 02/09/2023]
Abstract
Human ATP-binding cassette superfamily G member 2 (ABCG2) protein is a member of the ABC transporter family, which is responsible for multidrug resistance (MDR) in cancerous cells. MDR reduces the effectiveness of chemotherapy in breast cancer, which is one of the leading causes of death in women globally. MDR in cancer cells is one of the immediate signs of progression of resistance; thus, various anticancer drugs can be designed. To reduce MDR, we utilized the tetrahydro-β-carboline (THβC) compound library. We accomplished a three-dimensional quantitative structure-activity relationship (3D-QSAR), scaffold hopping to design a new library of compounds of THβC, and further molecular docking, induced-fit docking (IFD), molecular mechanics energies combined with generalized born and surface area continuum solvation (MM-GBSA), drug-like features, ADMET properties, and density functional theory (DFT) studies were performed. From these studies, the best 3D-QSAR model (r2 = 0.99, q2 = 0.92) was found, and the necessity of electrostatic, steric, and hydrophobic field effects were determined that could modulate bioactivity. Moreover, based on electrostatic, steric, and hydrophobic field notations, new THβC derivatives (3409) were designed. These findings might provide new insight for researchers to perform in vitro and in vivo studies for better antagonists against MDR in treating breast cancer.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shahnawaz Ahmad
- School of Biotechnology, College of Engineering and Technology, IFTM University, Moradabad, Uttar Pradesh, India
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Dinesh Gupta
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi, India
| | - Tanzeel Ahmed
- School of Biotechnology, College of Engineering and Technology, IFTM University, Moradabad, Uttar Pradesh, India
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
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Alsukaibi AKD, Alenezi KM, Haque A, Ahmad I, Saeed M, Verma M, Ansari IA, Hsieh MF. Chemical, biological and in silico assessment of date ( P. dactylifera L.) fruits grown in Ha'il region. Front Chem 2023; 11:1138057. [PMID: 36936534 PMCID: PMC10022733 DOI: 10.3389/fchem.2023.1138057] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 02/22/2023] [Indexed: 03/06/2023] Open
Abstract
Background: Dates palm (Phoenix dactylifera L.) fruits are among the most widely used fruits in the Middle East and African nations. Numerous researchers confirmed the presence of phytochemicals in P. dactylifera L. fruit and its by-products with broad-ranging biological activities. Objectives: In the present work, phytochemical and biological assessments of two different cultivars of date fruit (Shishi M1 and Majdool M2 grown in the Ha'il region of Saudi Arabia) have been carried out. Methods: Date fruits were extracted and analyzed by gas chromatography-mass spectrometry (GS-MS),liquid chromatography-mass spectrometry (LC-MS) and Fourier-transform infrared spectroscopy (FT-IR)techniques. The lyophilized methanolic extracts were analyzed for their in-vitro antiproliferative andcytotoxicity against colon cancer (HCT116) cell line. To identify the possible constituents responsible for the bioactivity, in-silico molecular docking and molecular dynamics (MD) simulation studies were carried out. Results: Both cultivars exhibited in-vitro anticancer activity (IC50 = 591.3 μg/mL and 449.9 μg/mL for M1 and M2, respectively) against colon cancer HCT-116 cells. The computational analysis results indicated procyanidin B2 and luteolin-7-O-rutinoside as the active constituents. Conclusion: Based on these results, we conclude that these cultivars could be a valuable source for developing health promoter phytochemicals, leading to the development of the Ha'il region, Saudi Arabia.
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Affiliation(s)
| | - Khalaf M. Alenezi
- Department of Chemistry, College of Science, University of Ha’il, Hail, Saudi Arabia
- *Correspondence: Khalaf M. Alenezi, ; Ashanul Haque, ; Ming-Fa Hsieh,
| | - Ashanul Haque
- Department of Chemistry, College of Science, University of Ha’il, Hail, Saudi Arabia
- *Correspondence: Khalaf M. Alenezi, ; Ashanul Haque, ; Ming-Fa Hsieh,
| | - Irfan Ahmad
- Department of Clinical Laboratory Science, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
| | - Mohd Saeed
- Department of Biology, College of Science, University of Ha’il, Hail, Saudi Arabia
| | - Mahima Verma
- Department of Biosciences, Integral University, Lucknow, India
| | | | - Ming-Fa Hsieh
- Department of Biomedical Engineering, Chung Yuan Christian University, Taoyuan City, Taiwan
- *Correspondence: Khalaf M. Alenezi, ; Ashanul Haque, ; Ming-Fa Hsieh,
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Asati V, Bharti SK, Das R, Kashaw V, Kashaw SK. Discovery of novel ALK2 inhibitors of pyrazolo-pyrimidines: A computational study. J Biomol Struct Dyn 2022; 40:10422-10436. [PMID: 34225569 DOI: 10.1080/07391102.2021.1944320] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
ALK2 is a serine/threonine kinase, involved in different signaling pathways and associated with cell proliferation and differentiation. The present study includes development of pharmacophore, 3-D QSAR, docking and virtual screening studies on 30 different pyrazolo[1,5-a]pyrimidine derivatives. The pharmacophore study provides ARRR_2 hypothesis with four different features essential for ALK2 kinase inhibitory activity. The 3 D-QSAR study determined the statistically significant model by using partial least-square regression (PLS) method with R2 value of 0.9711 and Q2 value of 0.6846. Validation of 3 D-QSAR has been performed by LOO cross-validation method where with R2CV value of 0.56. The virtual screening study on ZINC database provides compounds such as ZINC66091638, ZINC43524105, ZINC19458227 and ZINC72441013 involved good binding interactions (docking scores -8.91, -7.40, -8.43, and -9.47, respectively) with ALK2 kinase (PDB ID: 3Q4U). The docking study of pyrazolo-pyrimidines derivatives found potent compounds, 7i, 13r, 13d, and 21 with docking scores -9.83, -9.75, -9.76, and -9.75, respectively. The important interactions with amino acid residues were HID 286, ASN341. ADME properties further assist to provide important structural features of ALK2 kinase. The present study may be help to medicinal scientists in the direction to develop potent inhibitors against ALK2 kinase.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Vivek Asati
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, Moga, Punjab, India
| | - Sanjay K Bharti
- Institute of Pharmaceutical Sciences, Guru Ghasidas Vishwavidyalaya (A Central University), Bilaspur, Chhattisgarh, India
| | - Ratnesh Das
- Department of Chemistry, Dr. Harisingh Gour University (A Central University), Sagar, Madhya Pradesh, India
| | - Varsha Kashaw
- Sagar Institute of Pharmaceutical Sciences, Sagar, Madhya Pradesh, India
| | - Sushil Kumar Kashaw
- Department of Pharmaceutical Sciences, Dr. Harisingh Gour University (A Central University), Sagar, Madhya Pradesh, India
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11
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Ahmad S, Hassan MI, Gupta D, Dwivedi N, Islam A. Design and evaluation of pyrimidine derivatives as potent inhibitors of ABCG2, a breast cancer resistance protein. 3 Biotech 2022; 12:182. [PMID: 35875174 PMCID: PMC9296744 DOI: 10.1007/s13205-022-03231-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 06/18/2022] [Indexed: 11/25/2022] Open
Abstract
The protein ATP-binding cassette subfamily G member 2 (ABCG2) is one of the major factors behind multidrug resistance (MDR) in breast cancer. We performed three-dimensional quantitative structure-activity relationship (3D-QSAR) modelling, docking, and molecular dynamics (MD) simulation to design pyrimidine-based ABCG2 antagonists. The developed QSAR model (r 2 = 0.92, q 2 = 0.82, and good cross-validated r 2 = 0.73) dictate requirement of electrostatic, and hydrophobic fields for modulating bioactivity. Based on this rationale, we designed and screened 1010 new compounds, among them 2 (ND-510 and ND-500) exhibit excellent drug-like features. Comparative molecular docking, MM/GBSA and ADMET profiles were determined to understand the interactive poses, affinity, and drug-likeness of the designed compounds. Furthermore, MD simulations were performed with the ABCG2 receptor, and the results were compared with the two earlier synthesized active compounds. The outcomes of the study will help researchers to develop new antagonists for treatment of MDR breast cancer. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03231-1.
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Affiliation(s)
- Shahnawaz Ahmad
- School of Biotechnology, College of Engineering and Technology, IFTM University, Lodhipur-Rajput, Delhi Road (NH-24), Moradabad, Uttar Pradesh 244102 India
| | - Md. Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, 110025 India
| | - Dinesh Gupta
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi, 110067 India
| | - Neeraj Dwivedi
- School of Biotechnology, College of Engineering and Technology, IFTM University, Lodhipur-Rajput, Delhi Road (NH-24), Moradabad, Uttar Pradesh 244102 India
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, 110025 India
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12
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Ahamad S, Kanipakam H, Gupta D. Insights into the structural and dynamical changes of spike glycoprotein mutations associated with SARS-CoV-2 host receptor binding. J Biomol Struct Dyn 2022; 40:263-275. [PMID: 32851910 PMCID: PMC7484578 DOI: 10.1080/07391102.2020.1811774] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 08/13/2020] [Indexed: 12/13/2022]
Abstract
Novel Coronavirus or SARS-CoV-2 has received worldwide attention due to the COVID-19 pandemic, which originated in Wuhan, China leading to thousands of deaths to date. The SARS-CoV-2 Spike glycoprotein protein is one of the main focus of COVID-19 related research as it is a structural protein that facilitates its attachment, entry, and infection to the host cells. We have focused our work on mutations in two of the several functional domains in the virus spike glycoprotein, namely, receptor-binding domain (RBD) and heptad repeat 1 (HR1) domain. These domains are majorly responsible for the stability of spike glycoprotein and play a key role in the host cell attachment and infection. In our study, several mutations like R408I, L455Y, F486L, Q493N, Q498Y, N501T of RBD (319-591), and A930V, D936Y of HR1 (912-984) have been studied to examine its role on the spike glycoprotein native structure. Comparisons of MD simulations in the WT and mutants revealed a significant de-stabilization effect of the mutations on RBD and HR1 domains. We have investigated the impact of mapped mutations on the stability of the spike glycoprotein, before binding to the receptor, which may be consequential to its binding properties to the receptor and other ligands.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shahzaib Ahamad
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Hema Kanipakam
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Dinesh Gupta
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
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Hema K, Ahamad S, Joon HK, Pandey R, Gupta D. Atomic Resolution Homology Models and Molecular Dynamics Simulations of Plasmodium falciparum Tubulins. ACS OMEGA 2021; 6:17510-17522. [PMID: 34278137 PMCID: PMC8280665 DOI: 10.1021/acsomega.1c01988] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 05/21/2021] [Indexed: 05/14/2023]
Abstract
Microtubules are tubulin polymers present in the eukaryotic cytoskeleton essential for structural stability and cell division that are also roadways for intracellular transport of vesicles and organelles. In the human malaria parasite Plasmodium falciparum, apart from providing structural stability and cell division, microtubules also facilitate important biological activities crucial for parasite survival in hosts, such as egression and motility. Hence, parasite structures and processes involving microtubules are among the most important drug targets for discovering much-needed novel Plasmodium inhibitors. The current study aims to construct reliable and high-quality 3D models of α-, β-, and γ-tubulins using various modeling techniques. We identified a common binding pocket specific to Plasmodium α-, β-, and γ-tubulins. Molecular dynamics simulations confirmed the stability of the Plasmodium tubulin 3D structures. The models generated in the present study may be used for protein-protein and protein-drug interaction investigations targeted toward designing malaria parasite tubulin-specific inhibitors.
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Affiliation(s)
| | | | | | | | - Dinesh Gupta
- . Mobile: +91 9312304662. Office: +91 11 26742184
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Mushtaque M, Avecilla F, Ahmad I, Alharbi AM, Khan P, Ahamad S, Hassan MI. 5-Fluorouracil (5-FU)-based Aza-Michael addition product: A selective carbonic anhydrase IX inhibitor. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.129977] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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15
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Khan MW, Otaibi AA, Al-Zahrani SA, Alshammari EM, Haque A, Alouffi S, Khan WA, Khan SN. Experimental and theoretical insight into resistance to glycation of bovine serum albumin. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2020.129645] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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16
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Ahamad S, Hema K, Gupta D. Structural stability predictions and molecular dynamics simulations of RBD and HR1 mutations associated with SARS-CoV-2 spike glycoprotein. J Biomol Struct Dyn 2021; 40:6697-6709. [PMID: 33618621 DOI: 10.1080/07391102.2021.1889671] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The COVID-19 pandemic is caused by human transmission and infection of Severe Acute Respiratory Syndrome Corona Virus-2 (SARS-CoV-2). There is no trusted drug against the virus; hence, efforts are on discovering novel inhibitors for the virus. The entry of a SARS-CoV-2 virus particle into a host cell is initiated by its spike glycoprotein and host Angiotensin-Converting Enzyme 2 (ACE2) receptor interaction. Spike glycoprotein domains, namely, the Receptor Binding Domain (RBD) and Heptad Repeat (HR) domains, are essential for this activity. We have studied the impact of mutations such as A348T, N354D, D364Y, G476S, V483A, S494D in the RBD (319-591), and S939F, S940T, T941A, S943P (912-984) in the HR1 domains of spike glycoprotein. Summarily, we utilized the computational screening algorithms to rank the deleterious, damaging and disease-associated spike glycoprotein mutations. Subsequently, to understand the changes in conformation, flexibility and function of the spike glycoprotein mutants, Molecular Dynamics (MD) simulations were performed. The computational predictions and analysis of the MD trajectories suggest that the RBD and HR1 mutations induce significant phenotypic effects on the pre-binding spike glycoprotein structure, which are presumably consequential to its binding to the receptor and provides lead to design inhibitors against the binding.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shahzaib Ahamad
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Kanipakam Hema
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Dinesh Gupta
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
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Ahamad S, Kanipakam H, Birla S, Ali MS, Gupta D. Screening Malaria-box compounds to identify potential inhibitors against SARS-CoV-2 M pro, using molecular docking and dynamics simulation studies. Eur J Pharmacol 2020; 890:173664. [PMID: 33131721 PMCID: PMC7584923 DOI: 10.1016/j.ejphar.2020.173664] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 10/14/2020] [Accepted: 10/21/2020] [Indexed: 12/11/2022]
Abstract
Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2) Main protease (Mpro) is one of the vital drug targets amongst all the coronaviruses, as the protein is indispensable for virus replication. The study aimed to identify promising lead molecules against Mpro enzyme through virtual screening of Malaria Venture (MMV) Malaria Box (MB) comprising of 400 experimentally proven compounds. The binding affinities were studied using virtual screening based molecular docking, which revealed five molecules having the highest affinity scores compared to the reference molecules. Utilizing the established 3D structure of Mpro the binding affinity conformations of the docked complexes were studied by Molecular Dynamics (MD) simulations. The MD simulation trajectories were analysed to monitor protein deviation, relative fluctuation, atomic gyration, compactness covariance, residue-residue map and free energy landscapes. Based on the present study outcome, we propose three Malaria_box (MB) compounds, namely, MB_241, MB_250 and MB_266 to be the best lead compounds against Mpro activity. The compounds may be evaluated for their inhibitory activities using experimental techniques.
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Affiliation(s)
- Shahzaib Ahamad
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, 110067, India
| | - Hema Kanipakam
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, 110067, India
| | - Shweta Birla
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, 110067, India
| | - Md Shaukat Ali
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, 110067, India
| | - Dinesh Gupta
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, 110067, India.
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Naqvi AAT, Jairajpuri DS, Hussain A, Hasan GM, Alajmi MF, Hassan MI. Impact of glioblastoma multiforme associated mutations on the structure and function of MAP/microtubule affinity regulating kinase 4. J Biomol Struct Dyn 2020; 39:1781-1794. [DOI: 10.1080/07391102.2020.1738959] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Ahmad Abu Turab Naqvi
- Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Deeba Shamim Jairajpuri
- Department of Medical Biochemistry, College of Medicine and Medical Sciences, Arabian Gulf University, Manama, Bahrain
| | - Afzal Hussain
- Department of Pharmacognosy College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Gulam Mustafa Hasan
- Department of Biochemistry, College of Medicine, Prince Sattam Bin Abdulaziz University, Al-Kharj, Kingdom of Saudi Arabia
| | - Mohamed F. Alajmi
- Department of Pharmacognosy College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Md. Imtaiyaz Hassan
- Center for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
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Sardar R, Katyal N, Ahamad S, Jade DD, Ali S, Gupta D. In-silico profiling and structural insights into the impact of nSNPs in the P. falciparum acetyl-CoA transporter gene to understand the mechanism of drug resistance in malaria. J Biomol Struct Dyn 2020; 39:558-569. [PMID: 31903842 DOI: 10.1080/07391102.2020.1711807] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The continuous emergence of resistance to the available drugs poses major constraints in the development of effective therapeutics against malaria. Malaria drug resistance has been attributed to be the manifestation of numerous factors. For example, mutations in the parasite transporter protein acetyl-CoA transporter (Pfact) can remarkably affect its uptake affinity for a drug molecule against malaria, and hence enhance its susceptibility to resistance. To identify major contributors to its loss of functionality, we have thoroughly scrutinized eight such recently reported resistant mutants, via in-silico tools in terms of alterations in different properties. We performed molecular dynamics simulations of the selected Pfact mutants to gain deeper insights into the structural perturbation and dynamicity. Comparison of residue interaction network map of mutants with that of Wild type (WT) protein suggests structural changes as a result of the mutation(s) that translate into the weakening of intra-protein interactions, especially around the drug binding pocket. This, in turn, diminishes the affinity of drug molecules towards the binding site, which was validated by docking analysis. Finally, collating all the observations, we have delineated R108K mutant to deviate the most from WT protein, which, intriguingly suggests that replacing an amino acid with another of similar nature can even translate into greater functional effects as those with dissimilar substitutions.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rahila Sardar
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India.,Department of Biochemistry, Jamia Hamdard, New Delhi, India
| | - Nidhi Katyal
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Shahzaib Ahamad
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Dhananjay D Jade
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Shakir Ali
- Department of Biochemistry, Jamia Hamdard, New Delhi, India
| | - Dinesh Gupta
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
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