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For: Junaid M, Shah M, Khan A, Li CD, Khan MT, Kaushik AC, Ali A, Mehmood A, Nangraj AS, Choi S, Wei DQ. Structural-dynamic insights into the H. pylori cytotoxin-associated gene A (CagA) and its abrogation to interact with the tumor suppressor protein ASPP2 using decoy peptides. J Biomol Struct Dyn 2018;37:4035-4050. [PMID: 30328798 DOI: 10.1080/07391102.2018.1537895] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Number Cited by Other Article(s)
1
Zulfat M, Hakami MA, Hazazi A, Mahmood A, Khalid A, Alqurashi RS, Abdalla AN, Hu J, Wadood A, Huang X. Identification of novel NLRP3 inhibitors as therapeutic options for epilepsy by machine learning-based virtual screening, molecular docking and biomolecular simulation studies. Heliyon 2024;10:e34410. [PMID: 39170440 PMCID: PMC11336274 DOI: 10.1016/j.heliyon.2024.e34410] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 07/06/2024] [Accepted: 07/09/2024] [Indexed: 08/23/2024]  Open
2
Ajmal A, Shahab M, Waqas M, Zheng G, Zulfat M, Bin Jardan YA, Wondmie GF, Bourhia M, Ali I. In silico design of peptide inhibitors for Dengue virus to treat Dengue virus-associated infections. Sci Rep 2024;14:13130. [PMID: 38849372 PMCID: PMC11161489 DOI: 10.1038/s41598-024-63064-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 05/24/2024] [Indexed: 06/09/2024]  Open
3
Myrou A. Molecular Mechanisms and Treatment Strategies for Helicobacter pylori-Induced Gastric Carcinogenesis and Mucosa-Associated Lymphoid Tissue (MALT) Lymphoma. Cureus 2024;16:e60326. [PMID: 38883131 PMCID: PMC11177234 DOI: 10.7759/cureus.60326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/15/2024] [Indexed: 06/18/2024]  Open
4
Hanifa B, Bibi N, Sirajuddin M, Tiekink ERT, Kubicki M, Khan I, Bari A, Wadood A, Shams S. Synthesis, spectral characterisation, biocidal investigation, in-silico and molecular docking studies of 4-[(2-chloro-4-methylphenyl)carbamoyl]butanoic acid derived triorganotin(IV) compounds. J Biomol Struct Dyn 2024;42:1826-1845. [PMID: 37114651 DOI: 10.1080/07391102.2023.2204160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 04/08/2023] [Indexed: 04/29/2023]
5
M Alshabrmi F, Alatawi EA. Unraveling the mechanisms of Cefoxitin resistance in methicillin-resistant Staphylococcus aureus (MRSA): structural and molecular simulation-based insights. J Biomol Struct Dyn 2023:1-11. [PMID: 37811561 DOI: 10.1080/07391102.2023.2262591] [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: 06/14/2023] [Accepted: 09/17/2023] [Indexed: 10/10/2023]
6
Ajmal A, Ali Y, Khan A, Wadood A, Rehman AU. Identification of novel peptide inhibitors for the KRas-G12C variant to prevent oncogenic signaling. J Biomol Struct Dyn 2023;41:8866-8875. [PMID: 36300526 DOI: 10.1080/07391102.2022.2138550] [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: 07/05/2022] [Accepted: 10/15/2022] [Indexed: 10/31/2022]
7
Shahab M, Al-Madhagi H, Zheng G, Zeb A, Alasmari AF, Alharbi M, Alasmari F, Khan MQ, Khan M, Wadood A. Structure based virtual screening and molecular simulation study of FDA-approved drugs to inhibit human HDAC6 and VISTA as dual cancer immunotherapy. Sci Rep 2023;13:14466. [PMID: 37660065 PMCID: PMC10475047 DOI: 10.1038/s41598-023-41325-9] [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: 07/03/2023] [Accepted: 08/24/2023] [Indexed: 09/04/2023]  Open
8
Samad A, Khurshid B, Mahmood A, Rehman AU, Khalid A, Abdalla AN, Algarni AS, Wadood A. Identification of novel peptide inhibitors for oncogenic KRAS G12D as therapeutic options using mutagenesis-based remodeling and MD simulations. J Biomol Struct Dyn 2023;41:13425-13437. [PMID: 37010994 DOI: 10.1080/07391102.2023.2192298] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 01/22/2023] [Indexed: 04/04/2023]
9
Samad A, Ajmal A, Mahmood A, Khurshid B, Li P, Jan SM, Rehman AU, He P, Abdalla AN, Umair M, Hu J, Wadood A. Identification of novel inhibitors for SARS-CoV-2 as therapeutic options using machine learning-based virtual screening, molecular docking and MD simulation. Front Mol Biosci 2023;10:1060076. [PMID: 36959979 PMCID: PMC10028080 DOI: 10.3389/fmolb.2023.1060076] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 01/11/2023] [Indexed: 03/09/2023]  Open
10
Zhang Y, Li X, Shan B, Zhang H, Zhao L. Perspectives from recent advances of Helicobacter pylori vaccines research. Helicobacter 2022;27:e12926. [PMID: 36134470 DOI: 10.1111/hel.12926] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 07/25/2022] [Accepted: 08/17/2022] [Indexed: 12/09/2022]
11
Ghufran M, Khan HA, Ullah M, Ghufran S, Ayaz M, Siddiq M, Hassan SSU, Bungau S. In Silico Strategies for Designing of Peptide Inhibitors of Oncogenic K-Ras G12V Mutant: Inhibiting Cancer Growth and Proliferation. Cancers (Basel) 2022;14:4884. [PMID: 36230807 PMCID: PMC9564332 DOI: 10.3390/cancers14194884] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 10/02/2022] [Accepted: 10/03/2022] [Indexed: 12/12/2022]  Open
12
Suleman M, Umme-I-Hani S, Salman M, Aljuaid M, Khan A, Iqbal A, Hussain Z, Ali SS, Ali L, Sher H, Waheed Y, Wei DQ. Sequence-structure functional implications and molecular simulation of high deleterious nonsynonymous substitutions in IDH1 revealed the mechanism of drug resistance in glioma. Front Pharmacol 2022;13:927570. [PMID: 36188571 PMCID: PMC9523485 DOI: 10.3389/fphar.2022.927570] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 07/25/2022] [Indexed: 11/30/2022]  Open
13
Repositioning of experimentally validated anti-breast cancer peptides to target FAK-PAX complex to halt the breast cancer progression: a biomolecular simulation approach. Mol Divers 2022;27:603-618. [PMID: 35635599 DOI: 10.1007/s11030-022-10438-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 04/07/2022] [Indexed: 12/11/2022]
14
Ru Z, Yu M, Zhu Y, Chen Z, Zhang F, Zhang Z, Ding J. Immmunoinformatics-based design of a multi-epitope vaccine with CTLA-4 extracellular domain to combat Helicobacter pylori. FASEB J 2022;36:e22252. [PMID: 35294065 DOI: 10.1096/fj.202101538rr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 02/17/2022] [Accepted: 03/01/2022] [Indexed: 11/11/2022]
15
Gorostiola González M, Janssen APA, IJzerman AP, Heitman LH, van Westen GJP. Oncological drug discovery: AI meets structure-based computational research. Drug Discov Today 2022;27:1661-1670. [PMID: 35301149 DOI: 10.1016/j.drudis.2022.03.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 01/22/2022] [Accepted: 03/09/2022] [Indexed: 02/08/2023]
16
Babar Z, Khan M, Zahra M, Anwar M, Noor K, Hashmi HF, Suleman M, Waseem M, Shah A, Ali S, Ali SS. Drug similarity and structure-based screening of medicinal compounds to target macrodomain-I from SARS-CoV-2 to rescue the host immune system: a molecular dynamics study. J Biomol Struct Dyn 2022;40:523-537. [PMID: 32897173 PMCID: PMC7544951 DOI: 10.1080/07391102.2020.1815583] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Accepted: 08/21/2020] [Indexed: 01/17/2023]
17
Khan A, Umbreen S, Hameed A, Fatima R, Zahoor U, Babar Z, Waseem M, Hussain Z, Rizwan M, Zaman N, Ali S, Suleman M, Shah A, Ali L, Ali SS, Wei DQ. In Silico Mutagenesis-Based Remodelling of SARS-CoV-1 Peptide (ATLQAIAS) to Inhibit SARS-CoV-2: Structural-Dynamics and Free Energy Calculations. Interdiscip Sci 2021;13:521-534. [PMID: 34324157 PMCID: PMC8319699 DOI: 10.1007/s12539-021-00447-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 05/29/2021] [Accepted: 06/04/2021] [Indexed: 12/20/2022]
18
Hashmi HF, Waseem M, Ali SS, Hussain Z, Chen K. Structural and Biophysical Investigation of the Key Hotspots on the Surface of Epstein-Barr Nuclear Antigen 1 Essential for DNA Recognition and Pathogenesis. Front Mol Biosci 2021;8:664436. [PMID: 34268333 PMCID: PMC8275655 DOI: 10.3389/fmolb.2021.664436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 06/14/2021] [Indexed: 11/30/2022]  Open
19
Khan S, Hussain Z, Safdar M, Khan A, Wei DQ. Targeting the N-terminal domain of the RNA-binding protein of the SARS-CoV-2 with high affinity natural compounds to abrogate the protein-RNA interaction: a molecular dynamics study. J Biomol Struct Dyn 2021;40:6286-6294. [PMID: 33554747 DOI: 10.1080/07391102.2021.1882337] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
20
Feng X, Han L, Ma S, Zhao L, Wang L, Zhang K, Yin P, Guo L, Jing W, Li Q. Microbes in Tumoral In Situ Tissues and in Tumorigenesis. Front Cell Infect Microbiol 2020;10:572570. [PMID: 33330121 PMCID: PMC7732458 DOI: 10.3389/fcimb.2020.572570] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 10/23/2020] [Indexed: 12/14/2022]  Open
21
Khan A, Khan M, Saleem S, Babar Z, Ali A, Khan AA, Sardar Z, Hamayun F, Ali SS, Wei DQ. Phylogenetic Analysis and Structural Perspectives of RNA-Dependent RNA-Polymerase Inhibition from SARs-CoV-2 with Natural Products. Interdiscip Sci 2020;12:335-348. [PMID: 32617855 PMCID: PMC7332347 DOI: 10.1007/s12539-020-00381-9] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 06/19/2020] [Accepted: 06/23/2020] [Indexed: 01/18/2023]
22
Kaushik AC, Mehmood A, Dai X, Wei DQ. Pan-Cancer Analysis and Drug Formulation for GPR139 and GPR142. Front Pharmacol 2020;11:521245. [PMID: 33679382 PMCID: PMC7933564 DOI: 10.3389/fphar.2020.521245] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 11/23/2020] [Indexed: 02/03/2023]  Open
23
Molecular anatomy and pathogenic actions of Helicobacter pylori CagA that underpin gastric carcinogenesis. Cell Mol Immunol 2019;17:50-63. [PMID: 31804619 PMCID: PMC6952403 DOI: 10.1038/s41423-019-0339-5] [Citation(s) in RCA: 133] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 11/13/2019] [Accepted: 11/13/2019] [Indexed: 12/15/2022]  Open
24
Junaid M, Li CD, Shah M, Khan A, Guo H, Wei DQ. Extraction of molecular features for the drug discovery targeting protein-protein interaction of Helicobacter pylori CagA and tumor suppressor protein ASSP2. Proteins 2019;87:837-849. [PMID: 31134671 DOI: 10.1002/prot.25748] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 05/04/2019] [Accepted: 05/22/2019] [Indexed: 12/13/2022]
25
Xu H, Tang Z, Zuo Y, Xiong F, Chen K, Jiang H, Luo C, Zhang H. Molecular dynamics simulation revealed the intrinsic conformational change of cellular inhibitor of apoptosis protein-1. J Biomol Struct Dyn 2019;38:975-984. [PMID: 30843765 DOI: 10.1080/07391102.2019.1591303] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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