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Mohammadnejadi E, Razzaghi-Asl N. In silico target specific design of potential quinazoline-based anti-NSCLC agents. J Biomol Struct Dyn 2023; 41:10725-10736. [PMID: 36826424 DOI: 10.1080/07391102.2023.2183029] [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: 08/13/2022] [Accepted: 12/07/2022] [Indexed: 02/25/2023]
Abstract
Non-small cell lung cancer (NSCLC) accounts for 85% of all lung cancers. In spite of great advances, treatment of the disease is a medical challenge. Epidermal-growth factor receptor (EGFR) has been taken as a promising cell surface target to develop anti-NSCLC therapies. The main bottleneck to attain clinical efficacy with current EGFR tyrosine kinase inhibitors (EGFR-TKIs) is the rapid spread of oncogenic mutations. Numerous efforts have been made for the synthesis of diverse EGFR-TKIs against resistance-conferring mutations. One of the best strategies to design potent agents would be to explore existing anti-NSCLC drugs at the nonclinical development stage and prioritize privileged structural patterns. Within current study, conformational stability of clinically frequent EGFR mutants (G719S, T790M, L858R and a double mutant form L858R/T790M) were validated via DynaMut and missense3D computational servers. Subsequently, structure activity relationship (SAR) and scaffold similarity inquiry were used to rationally propose a few erlotinib analogues. Intended molecules were subjected to molecular docking and top-scored binders were further analyzed through 50-ns all atom molecular dynamics (MD) simulations to infer the dynamic behavior. The aim was to offer potential binders to overwhelm clinically frequent EGFR-TK mutants. The linear interaction energy (LIE) method was applied to compute the binding free energies between EGFR and intended ligands. For this purpose, MD-based conformational sampling of ligand-enzyme complexes and ligand-water associations were used to acquire thermodynamic energy averages. Though mechanistic details are to be explored, results of the current study identify synthetically accessible quinazoline small molecules with potential affinity toward frequent EGFR-TK mutants.[Figure: see text]Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Elaheh Mohammadnejadi
- Students Research Committee, School of Pharmacy, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Nima Razzaghi-Asl
- Department of Medicinal Chemistry, School of Pharmacy, Ardabil University of Medical Sciences, Ardabil, Iran
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Kumar R, Kumar R, Goel H, Kumar S, Ningombam SS, Haider I, Agrawal U, Deo S, Gogia A, Batra A, Sharma A, Mathur S, Ranjan A, Chopra A, Hussain S, Tanwar P. Whole exome sequencing identifies novel variants of PIK3CA and validation of hotspot mutation by droplet digital PCR in breast cancer among Indian population. Cancer Cell Int 2023; 23:236. [PMID: 37821962 PMCID: PMC10568783 DOI: 10.1186/s12935-023-03075-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 09/20/2023] [Indexed: 10/13/2023] Open
Abstract
BACKGROUND Breast cancer (BC) is the most common malignancy with very high incidence and relatively high mortality in women. The PIK3CA gene plays a pivotal role in the pathogenicity of breast cancer. Despite this, the mutational status of all exons except exons 9 and 20 still remains unknown. METHODS This study uses the whole exome sequencing (WES) based approach to identify somatic PIK3CA mutations in Indian BC cohorts. The resultant hotspot mutations were validated by droplet digital PCR (ddPCR). Further, molecular dynamics (MD) simulation was applied to elucidate the conformational and functional effects of hotspot position on PIK3CA protein. RESULTS In our cohort, PIK3CA showed a 44.4% somatic mutation rate and was among the top mutated genes. The mutations of PIK3CA were confined in Exons 5, 9, 11, 18, and 20, whereas the maximum number of mutations lies within exons 9 and 20. A total of 9 variants were found in our study, of which 2 were novel mutations observed on exons 9 (p.H554L) and 11 (p.S629P). However, H1047R was the hotspot mutation at exon 20 (20%). In tumor tissues, there was a considerable difference between copy number of wild-type and H1047R mutant was detected by ddPCR. Significant structural and conformational changes were observed during MD simulation, induced due to point mutation at H1047R/L position. CONCLUSIONS The current study provides a comprehensive view of novel as well as reported single nucleotide variants (SNVs) in PIK3CA gene associated with Indian breast cancer cases. The mutation status of H1047R/L could serve as a prognostic value in terms of selecting targeted therapy in BC.
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Affiliation(s)
- Rahul Kumar
- Dr B. R. A.-Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India
| | - Rakesh Kumar
- Dr B. R. A.-Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India
| | - Harsh Goel
- Dr B. R. A.-Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India
| | - Sonu Kumar
- Department of Gastroenterology & HNU, All India Institute of Medical Sciences, New Delhi, India
| | - Somorjit Singh Ningombam
- Dr B. R. A.-Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India
| | - Imran Haider
- Dr B. R. A.-Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India
| | - Usha Agrawal
- National Institute of Pathology, New Delhi, India
| | - Svs Deo
- Dr B. R. A.-Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India
| | - Ajay Gogia
- Dr B. R. A.-Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India
| | - Atul Batra
- Dr B. R. A.-Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India
| | - Ashok Sharma
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Sandeep Mathur
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
| | - Amar Ranjan
- Dr B. R. A.-Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India
| | - Anita Chopra
- Dr B. R. A.-Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India
| | - Showket Hussain
- Division of Molecular Oncology, National Institute of Cancer Prevention and Research, Noida, India
| | - Pranay Tanwar
- Dr B. R. A.-Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India.
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Joshi K, Kaur S, Kumar R. Cytochrome P450 2C19 gene polymorphisms (CYP2C19*2 and CYP2C19*3) in chronic myeloid leukemia patients: in vitro and in silico studies. J Biomol Struct Dyn 2021; 40:9389-9402. [PMID: 34060427 DOI: 10.1080/07391102.2021.1929491] [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: 12/14/2022]
Abstract
Polymorphisms in the CYP2C19 have a huge impact on drug processing, out of which CYP2C19*2 and CYP2C19*3 are the most common variants associated with reduced metabolism of drugs. Mechanism by which two variants contribute in poor metabolization of drugs and cancer is not well understood. Here, we hypothesized that the mutations in CYP2C19 gene might affect the risk of chronic myeloid leukemia patients (CML). Present study has two main objectives: first to investigate the allele frequencies of CYP2C19*2 and CYP2C19*3 associated gene polymorphisms in CML patients and to elucidate the structural stability, conformation and functions of protein encoded by such variants. Genotyping of CYP2C19 was performed in 103 CML patients and 103 matched healthy controls. Heterozygous genotype of CYP2C19*2 was higher in CML patients (13.59%) than the controls (4.85%). Whereas, CYP2C19*3 allele frequency was not observed in cases as well as in controls. Furthermore, molecular dynamics (MD) simulation was applied to monitor the structural and conformational effect of above mutants. MD simulation results demonstrated that these mutants formed unstable proteins with distorted conformations, altered residues network and affected drug binding site which led to malfunction of mutant proteins. Hence, the study provides the role of CYP2C19 gene polymorphisms in susceptibility to CML population and explored the molecular basis of malignancies caused which may aid in the development of precise medicine or adjusting the drug dosages so as to reduce the chemotherapeutic side effects.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Kaishiv Joshi
- Department of Human Genetics, Punjabi University, Patiala, India
| | - Satbir Kaur
- Department of Human Genetics, Punjabi University, Patiala, India
| | - Rakesh Kumar
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
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Kumar R, Kumar R, Tanwar P. Structural based screening of potential inhibitors of SMAD4: a step towards personalized medicine for gall bladder and other associated cancers. Mol Divers 2021; 25:1945-1961. [PMID: 33751339 DOI: 10.1007/s11030-021-10210-w] [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: 10/21/2020] [Accepted: 03/14/2021] [Indexed: 12/24/2022]
Abstract
Gall bladder cancer (GBC) is an aggressive and most common malignancy of biliary tract lacking effective treatment due to unavailability of suitable biomarkers and therapeutics. SMAD4 is an essential mediator of transforming growth factor-β pathway involved in various cellular processes like growth, differentiation and apoptosis and also recognized as therapeutic target for GBC and other gastrointestinal tract cancers. In the present study, 3D structure of SMAD4 mutants was optimized through molecular dynamics simulation (MDS) along with wildtype. Furthermore, binding site of protein was predicted through hybrid approach and structural based virtual screening against two drug libraries was performed followed by docking. MDS of top docking score protein-ligand complexes were carried, and binding free energy was rescored. Two potential inhibitors, namely ZINC2098840 and ZINC8789167, were screened that displayed higher binding affinity towards mutant proteins compared with wildtype and both hydrophilic as well as hydrophobic interactions play a crucial role during protein-ligand binding. Current study identified novel and potent inhibitors of SMAD4 mutant that could be used as a drug candidate for the development of personalized medicine for gall bladder and other associated cancers.
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Affiliation(s)
- Rakesh Kumar
- Dr.B.R.A.-Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Rahul Kumar
- Dr.B.R.A.-Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Pranay Tanwar
- Dr.B.R.A.-Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, 110029, India.
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Ali A, Khan MT, Khan A, Ali S, Chinnasamy S, Akhtar K, Shafiq A, Wei DQ. Pyrazinamide resistance of novel mutations in pncA and their dynamic behavior. RSC Adv 2020; 10:35565-35573. [PMID: 35515677 PMCID: PMC9056903 DOI: 10.1039/d0ra06072k] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Accepted: 08/25/2020] [Indexed: 11/21/2022] Open
Abstract
Pyrazinamide (PZA) is one of the essential anti-mycobacterium drugs, active against non-replicating Mycobacterium tuberculosis (MTB) isolates. PZA is converted into its active state, called pyrazinoic acid (POA), by action of pncA encoding pyrazinamidase (PZase). In the majority of PZA-resistance isolates, pncA harbored mutations in the coding region. In our recent report, we detected a number of novel variants in PZA-resistance (PZAR) MTB isolates, whose resistance mechanisms were yet to be determined. Here we performed several analyses to unveil the PZAR mechanism of R123P, T76P, G150A, and H71R mutants (MTs) through molecular dynamics (MD) simulations. In brief, culture positive MTB isolates were subjected to PZA susceptibility tests using the WHO recommended concentration of PZA (100 μg ml−1). The PZAR samples were screened for mutations in pncA along sensitive isolates through polymerase chain reactions and sequencing. A large number of variants (GeneBank accession no. MH461111), including R123P, T76P, G150A, and H71R, have been spotted in more than 70% of isolates. However, the mechanism of PZAR for mutants (MTs) R123P, T76P, G150A, and H71R was unknown. For the MTs and native PZase structures (WT), thermodynamic properties were compared using molecular dynamics simulations for 100 ns. The MTs structural activity was compared to the WT. Folding effect and pocket volume variations have been detected when comparing between WT and MTs. Geometric matching further confirmed the effect of R123P, T76P, G150A, and H71R mutations on PZase dynamics, making them vulnerable for activating the pro-drug into POA. This study offers a better understanding for management of PZAR TB. The results may be used as alternative diagnostic tools to infer PZA resistance at a structural dynamics level. We performed several analyses to unveil the pyrazinamide-resistance mechanism of R123P, T76P, G150A, and H71R mutants through molecular dynamics simulations.![]()
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Affiliation(s)
- Arif Ali
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, and Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Shanghai Jiao Tong University 800 Dongchuan Road Shanghai, Minhang District Shanghai 200240 China +86-21-3420-4573
| | - Muhammad Tahir Khan
- Department of Bioinformatics and Biosciences, Capital University of Science and Technology Pakistan
| | - Abbas Khan
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, and Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Shanghai Jiao Tong University 800 Dongchuan Road Shanghai, Minhang District Shanghai 200240 China +86-21-3420-4573
| | - Sajid Ali
- Quaid-i-Azam University Islamabad, Provincial Tuberculosis Reference Laboratory Hayatabad Medical Complex Peshawar Pakistan
| | - Sathishkumar Chinnasamy
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, and Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Shanghai Jiao Tong University 800 Dongchuan Road Shanghai, Minhang District Shanghai 200240 China +86-21-3420-4573
| | - Khalid Akhtar
- National University of Science and Technology Pakistan
| | - Athar Shafiq
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, and Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Shanghai Jiao Tong University 800 Dongchuan Road Shanghai, Minhang District Shanghai 200240 China +86-21-3420-4573
| | - Dong-Qing Wei
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, and Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Shanghai Jiao Tong University 800 Dongchuan Road Shanghai, Minhang District Shanghai 200240 China +86-21-3420-4573.,Peng Cheng Laboratory Vanke Cloud City Phase I Building 8, Xili Street, Nanshan District Shenzhen Guangdong 518055 China
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