1
|
Yang L, Zhao H, Yuan F, Chen M, Ma N, Yin Z, Liu H, Guo Y. Computational study on the binding mechanism of allosteric drug TNO155 inhibiting SHP2 E76A. Mol Divers 2024:10.1007/s11030-024-10881-1. [PMID: 38807000 DOI: 10.1007/s11030-024-10881-1] [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: 10/26/2023] [Accepted: 04/15/2024] [Indexed: 05/30/2024]
Abstract
E76A mutations of SHP2 have been reported to associate with genetic developmental diseases and cancers, and TNO155 is one of the effective inhibitors targeted to the allosteric site 1, which has already entered the clinical stage. However, the detailed binding mechanism between them still needs further clarification at micro-atomic level. In this study, the binding mechanism of TNO155 inhibiting SHP2E76A and the superiorities of TNO155 at binding affinity and dynamic interactive behavior with SHP2E76A were probed utilizing a series of computational drug design technologies. The results show that SHP2E76A forms tighter interaction with TNO155 compared to SHP099. SHP2E76A-TNO155 exhibits the largest electrostatic interaction among all complex systems, which can be manifested by the strong hydrogen bond interactions formed by two electrically charged residues, Arg111 and Glu250. Notably, in SHP2E76A-TNO155 system, Asp489 makes an additional substantial beneficial contribution. The E76A mutation brings stronger residue positive correlation and a larger conformation fluctuation between N-CH2 and PTP domains, resulting in tighter binding between TNO155 and SHP2E76A. This study offers valuable insights for the further design and development of novel SHP2E76A allosteric inhibitors.
Collapse
Affiliation(s)
- Longhua Yang
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China.
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou, 450001, Henan, China.
| | - Huijian Zhao
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Fanru Yuan
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Mengguo Chen
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Nannan Ma
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Zhili Yin
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
| | - Hongmin Liu
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou, 450001, Henan, China
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou, 450001, China
- Key Laboratory of Henan Province for Drug Quality and Evaluation, Zhengzhou University, Zhengzhou, 450001, China
- Institute of Drug Discovery and Development, Zhengzhou University, Zhengzhou, 450001, China
| | - Yong Guo
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China.
| |
Collapse
|
2
|
Elamin G, Aljoundi A, Alahmdi MI, Abo-Dya NE, Soliman MES. Revealing the Role of the Arg and Lys in Shifting Paradigm from BTK Selective Inhibition to the BTK/HCK Dual Inhibition - Delving into the Inhibitory Activity of KIN-8194 against BTK, and HCK in the Treatment of Mutated BTKCys481 Waldenström Macroglobulinemia: A Computational Approach. Anticancer Agents Med Chem 2024; 24:813-825. [PMID: 36752293 DOI: 10.2174/1871520623666230208102609] [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: 07/22/2022] [Revised: 10/30/2022] [Accepted: 12/08/2022] [Indexed: 02/09/2023]
Abstract
BACKGROUND Despite the early success of Bruton's tyrosine kinase (BTK) inhibitors in the treatment of Waldenström macroglobulinemia (WM), these single-target drug therapies have limitations in their clinical applications, such as drug resistance. Several alternative strategies have been developed, including the use of dual inhibitors, to maximize the therapeutic potential of these drugs. OBJECTIVE Recently, the pharmacological activity of KIN-8194 was repurposed to serve as a 'dual-target' inhibitor of BTK and Hematopoietic Cell Kinase (HCK). However, the structural dual inhibitory mechanism remains unexplored, hence the aim of this study. METHODS Conducting predictive pharmacokinetic profiling of KIN-8194, as well as demonstrating a comparative structural mechanism of inhibition against the above-mentioned enzymes. RESULTS Our results revealed favourable binding affinities of -20.17 kcal/mol, and -35.82 kcal/mol for KIN-8194 towards HCK and BTK, respectively. Catalytic residues Arg137/174 and Lys42/170 in BTK and Arg303 and Lys75/173/244/247 in HCK were identified as crucial mediators of the dual binding mechanism of KIN-8194, corroborated by high per-residue energy contributions and consistent high-affinity interactions of these residues. Prediction of the pharmacokinetics and physicochemical properties of KIN-8194 further established its inhibitory potential, evidenced by the favourable absorption, metabolism, excretion, and minimal toxicity properties. Structurally, KIN-8194 impacted the stability, flexibility, solvent-accessible surface area, and rigidity of BTK and HCK, characterized by various alterations observed in the bound and unbound structures, which proved enough to disrupt their biological function. CONCLUSION These structural insights provided a baseline for the understanding of the dual inhibitory activity of KIN- 8194. Establishing the cruciality of the interactions between the KIN-8194 and Arg and Lys residues could guide the structure-based design of novel dual BTK/HCK inhibitors with improved therapeutic activities.
Collapse
Affiliation(s)
- Ghazi Elamin
- Department of Pharmaceutical Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa
| | - Aimen Aljoundi
- Department of Pharmaceutical Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa
| | - Mohamed I Alahmdi
- Department of Chemistry, Faculty of Science, University of Tabuk, Tabuk, 7149, Saudi Arabia
| | - Nader E Abo-Dya
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Tabuk University, Tabuk, 71491, Saudi Arabia
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Zagazig University, Zagazig, Egypt
| | - Mahmoud E S Soliman
- Department of Pharmaceutical Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa
| |
Collapse
|
3
|
Rahimi M, Taghdir M, Abasi Joozdani F. Dynamozones are the most obvious sign of the evolution of conformational dynamics in HIV-1 protease. Sci Rep 2023; 13:14179. [PMID: 37648682 PMCID: PMC10469195 DOI: 10.1038/s41598-023-40818-x] [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: 02/21/2023] [Accepted: 08/17/2023] [Indexed: 09/01/2023] Open
Abstract
Proteins are not static but are flexible molecules that can adopt many different conformations. The HIV-1 protease is an important target for the development of therapies to treat AIDS, due to its critical role in the viral life cycle. We investigated several dynamics studies on the HIV-1 protease families to illustrate the significance of examining the dynamic behaviors and molecular motions for an entire understanding of their dynamics-structure-function relationships. Using computer simulations and principal component analysis approaches, the dynamics data obtained revealed that: (i) The flap regions are the most obvious sign of the evolution of conformational dynamics in HIV-1 protease; (ii) There are dynamic structural regions in some proteins that contribute to the biological function and allostery of proteins via appropriate flexibility. These regions are a clear sign of the evolution of conformational dynamics of proteins, which we call dynamozones. The flap regions are one of the most important dynamozones members that are critical for HIV-1 protease function. Due to the existence of other members of dynamozones in different proteins, we propose to consider dynamozones as a footprint of the evolution of the conformational dynamics of proteins.
Collapse
Affiliation(s)
- Mohammad Rahimi
- Department of Biophysics, Faculty of Biological Science, Tarbiat Modares University, Tehran, 14115_111, Iran
| | - Majid Taghdir
- Department of Biophysics, Faculty of Biological Science, Tarbiat Modares University, Tehran, 14115_111, Iran.
| | - Farzane Abasi Joozdani
- Department of Biophysics, Faculty of Biological Science, Tarbiat Modares University, Tehran, 14115_111, Iran
| |
Collapse
|
4
|
Panda G, Ray A. Comparative Structural and Dynamics Study of Free and gRNA-bound FnCas9 and SpCas9 Proteins. Comput Struct Biotechnol J 2022; 20:4172-4184. [PMID: 36016716 PMCID: PMC9389198 DOI: 10.1016/j.csbj.2022.07.041] [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: 03/31/2022] [Revised: 07/25/2022] [Accepted: 07/25/2022] [Indexed: 12/04/2022] Open
Abstract
gRNA binding caused Cas9 to open up, exposing hydrophobic residues. Concerted domain movement was observed in both SpCas9 and FnCas9. gRNA binding led to decrease in helicity and increase in structural transitions. High binding affinity of FnCas9 with gRNA is mostly due to electrostatic interaction. Arginine-helix has shown a pivotal role in the binding of gRNA in FnCas9 protein.
The introduction of CRISPR/Cas9 based gene editing has greatly accelerated therapeutic genome editing. However, the off-target DNA cleavage by CRISPR/Cas9 protein hampers its clinical translation, hindering its widespread use as a programmable genome editing tool. Although Cas9 variants with better mismatch discrimination have been developed, they have significantly lower rates of on-target DNA cleavage. Here, we have compared the dynamics of a more specific naturally occurring Cas9 from Francisella novicida (FnCas9) to the most widely used, SpCas9 protein. Long-scale atomistic MD simulation of free and gRNA bound forms of both the Cas9 proteins was performed, and their domain rearrangements and binding affinity with gRNA were compared to decipher the possible reason behind the enhanced specificity of FnCas9 protein. The greater binding affinity with gRNA, high domain electrostatics, and more volatility of FnCas9 than SpCas9 may explain its increased specificity and lower tolerance for mismatches.
Collapse
|
5
|
Elamin G, Aljoundi A, Soliman MES. Co-Binding of JQ1 and Venetoclax Exhibited Synergetic Inhibitory Effect for Cancer Therapy; Potential Line of Treatment for the Waldenström Macroglobulinemia Lymphoma. Chem Biodivers 2022; 19:e202100845. [PMID: 35610180 DOI: 10.1002/cbdv.202100845] [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: 10/19/2021] [Accepted: 05/24/2022] [Indexed: 11/11/2022]
Abstract
In recent times, the development of combination therapy has been a focal point in drug discovery. This article explores the potential synergistic effect of co-administration of Bcl2 inhibitor Venetoclax and BET inhibitor JQ1. We envisioned that the 'dual-site'-binding of Bcl2 has significant prospects and paves the way for the next round of rational design of potent Waldenström macroglobulinemia (WM) therapy. The preferential binding mechanisms of the multi-catalytic sites of the Bcl2 enzyme have been a subject of debate in the literature. This study conducted a systematic procedure to explore the preferred binding modes and the structural effects of co-binding at each catalytic active site. Interestingly, a mutual enhanced binding effect was observed - Venetoclax increased the binding affinity of JQ1 by 11.5 %, while JQ1 boosted the binding affinity of Venetoclax by 16.3 % when compared with individual inhibition of each drug. This synergistic binding effect has significantly increased protein stability, with substantial correlated movements and multiple van der Waals interactions. The structural and thermodynamic insights unveiled in this report would assist the future design of improved combined therapy against WM.
Collapse
Affiliation(s)
- Ghazi Elamin
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa
| | - Aimen Aljoundi
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa
| | - Mahmoud E S Soliman
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa
| |
Collapse
|
6
|
Elamin G, Aljoundi A, Soliman MES. Multi-catalytic Sites Inhibition of Bcl2 Induces Expanding of Hydrophobic Groove: A New Avenue Towards Waldenström Macroglobulinemia Therapy. Protein J 2022; 41:201-215. [PMID: 35237907 DOI: 10.1007/s10930-022-10046-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/14/2022] [Indexed: 11/29/2022]
Abstract
B-cell lymphoma 2 (Bcl2) is a key protein regulator of apoptosis. The hydrophobic groove in Bcl2 is a unique structural feature to this class of enzymes and found to have a profound impact on protein overall structure, function, and dynamics. Dynamics of the hydrophobic groove is an essential determinant of the catalytic activity of Bcl2, an implicated protein in Waldenström macroglobulinemia (WM). The mobility of α3-α4 helices around the catalytic site of the protein remains crucial to its activity. The preferential binding mechanisms of the multi-catalytic sites of the Bcl2 enzyme have been a subject of debate in the literature. In addition to our previous report on the same protein, herein, we further investigate the preferential binding modes and the conformational implications of Venetoclax-JQ1 dual drug binding at both catalytic active sites of Bcl2. Structural analysis revealed asymmetric α3-α4 helices movement with the expansion of the distance between the α3 and α4 helix in Venetoclax-JQ1 dual inhibition by 15.2% and 26.3%, respectively when compared to JQ1 and Venetoclax individual drug inhibition-resulting in remarkable widening of hydrophobic groove. Moreso, a reciprocal enhanced binding effect was observed: Venetoclax increased the binding affinity of JQ1 by 11.5%, while the JQ1 fostered the binding affinity of Venetoclax by 16.3% compared with individual inhibition of each drug. This divergence has also resulted in higher protein stability, and prominent correlated motions were observed with the least fluctuations and multiple van der Waals interactions. Findings offer vital conformational dynamics and structural mechanisms of enzyme-single ligand and enzyme-dual ligand interactions, which could potentially shift the current therapeutic protocol of Waldenström macroglobulinemia.
Collapse
Affiliation(s)
- Ghazi Elamin
- Molecular Bio-Computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa
| | - Aimen Aljoundi
- Molecular Bio-Computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa
| | - Mahmoud E S Soliman
- Molecular Bio-Computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus, Durban, 4001, South Africa.
| |
Collapse
|
7
|
Hu LC, Ding CH, Li HY, Li ZZ, Chen Y, Li LP, Li WZ, Liu WS. Identification of potential target endoribonuclease NSP15 inhibitors of SARS-COV-2 from natural products through high-throughput virtual screening and molecular dynamics simulation. J Food Biochem 2022; 46:e14085. [PMID: 35128681 PMCID: PMC9114918 DOI: 10.1111/jfbc.14085] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 12/28/2021] [Accepted: 01/04/2022] [Indexed: 12/14/2022]
Abstract
SARS‐CoV‐2 wreaks havoc around the world, triggering the COVID‐19 pandemic. It has been confirmed that the endoribonuclease NSP15 is crucial to the viral replication, and thus identified as a potential drug target against COVID‐19. The NSP15 protein was used as the target to conduct high‐throughput virtual screening on 30,926 natural products from the NPASS database to identify potential NSP15 inhibitors. And 100 ns molecular dynamics simulations were performed on the NSP15 and NSP15‐NPC198199 system. In all, 10 natural products with high docking scores with NSP15 protein were obtained, among which compound NPC198199 scored the highest. The analysis of the binding mode between NPC198199 and NSP15 found that NPC198199 would form H‐bond interactions with multiple key residues at the catalytic site. Subsequently, a series of post‐dynamics simulation analyses (including RMSD, RMSF, PCA, DCCM, RIN, binding free energy, and H‐bond occupancy) were performed to further explore inhibitory mechanism of compound NPC198199 on NSP15 protein at the molecular level. The research strongly indicates that the 10 natural compounds screened can be used as potential inhibitors of NSP15, and provides valuable information for the subsequent drug discovery of anti‐SARS‐CoV‐2.
Collapse
Affiliation(s)
- Liang-Chang Hu
- Department of Oncology, Affiliated Hospital of Weifang Medical University, Weifang, China
| | - Chuan-Hua Ding
- Shandong Key Laboratory of Clinical Applied Pharmacology, Department of Pharmacy, Affiliated Hospital of Weifang Medical University, Weifang, China
| | - Hong-Ying Li
- Shandong Key Laboratory of Clinical Applied Pharmacology, Department of Pharmacy, Affiliated Hospital of Weifang Medical University, Weifang, China
| | - Zhen-Zhen Li
- Shandong Key Laboratory of Clinical Applied Pharmacology, Department of Pharmacy, Affiliated Hospital of Weifang Medical University, Weifang, China
| | - Ying Chen
- School of Pharmacy, Weifang Medical University, Weifang, China
| | - Li-Peng Li
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Wan-Zhong Li
- School of Pharmacy, Weifang Medical University, Weifang, China
| | - Wen-Shan Liu
- Shandong Key Laboratory of Clinical Applied Pharmacology, Department of Pharmacy, Affiliated Hospital of Weifang Medical University, Weifang, China
| |
Collapse
|
8
|
Elamin G, Aljoundi A, Soliman ME. A synergistic multitargeted of BET and HDAC: an intra-molecular mechanism of communication in treatment of Waldenström macroglobulinemia. MOLECULAR SIMULATION 2021. [DOI: 10.1080/08927022.2021.2005248] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Ghazi Elamin
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Aimen Aljoundi
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Mahmoud E.S. Soliman
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| |
Collapse
|
9
|
Habib I, Khan S, Mohammad T, Hussain A, Alajmi MF, Rehman T, Anjum F, Hassan MI. Impact of non-synonymous mutations on the structure and function of telomeric repeat binding factor 1. J Biomol Struct Dyn 2021; 40:9053-9066. [PMID: 33982644 DOI: 10.1080/07391102.2021.1922313] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Telomeric repeat binding factor 1 (TRF1) is one of the major components of the shelterin complex. It directly binds to the telomere and controls its function by regulating the telomerase acting on it. Several variations are reported in the TRF1 gene; some are associated with variety of diseases. Here, we have studied the structural and functional significance of these variations in the TRFH domain of TRF1. We have used cutting-edge computational methods such as SIFT, PolyPhen-2, PROVEAN, Mutation Assessor, mCSM, SDM, STRUM, MAESTRO, and DUET to predict the effects of 124 mutations in the TRFH domain of TRF1. Out of 124 mutations, we have identified 12 deleterious mutations with high confidence based on their prediction. To see the impact of the finally selected mutations on the structure and stability of TRF1, all-atom molecular dynamics (MD) simulations on TRF1-Wild type (WT), L79R and P150R mutants for 200 ns were carried out. A significant conformational change in the structure of the P150R mutant was observed. Our integrated computational study provides a comprehensive understanding of structural changes in TRF1 incurred due to the mutations and subsequent function, leading to the progression of many diseases.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Insan Habib
- Department of Computer Science, Jamia Millia Islamia, New Delhi, India
| | - Shama Khan
- Drug Discovery and Development Centre (H3D), University of Cape Town, Rondebosch, South Africa
| | - Taj Mohammad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Afzal Hussain
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Mohamed F Alajmi
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Tabish Rehman
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Farah Anjum
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| |
Collapse
|
10
|
Wang L, Wang Y, Yang Z, Xu S, Li H. Binding Selectivity of Inhibitors toward Bromodomains BAZ2A and BAZ2B Uncovered by Multiple Short Molecular Dynamics Simulations and MM-GBSA Calculations. ACS OMEGA 2021; 6:12036-12049. [PMID: 34056358 PMCID: PMC8154142 DOI: 10.1021/acsomega.1c00687] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 04/19/2021] [Indexed: 06/12/2023]
Abstract
Two Bromodomain-Containing proteins BAZ2A and BAZ2B are responsible for remodeling chromatin and regulating noncoding RNAs. As for our current studies, integration of multiple short molecular dynamics simulations (MSMDSs) with molecular mechanics generalized Born surface area (MM-GBSA) method is adopted for insights into binding selectivity of three small molecules D8Q, D9T and UO1 to BAZ2A against BAZ2B. The calculations of MM-GBSA unveil that selectivity of inhibitors toward BAZ2A and BAZ2B highly depends on the enthalpy changes and the details uncover that D8Q has better selectivity toward BAZ2A than BAZ2B, D9T more favorably bind to BAZ2B than BAZ2A, and UO1 does not show obvious selectivity toward these two proteins. The analysis of interaction network between residues and inhibitors indicates that seven residues are mainly responsible for the selectivity of D8Q, six residues for D9T and four residues provide significant contributions to associations of UO1 with two proteins. Moreover the analysis of interaction network not only reveals warm spots of inhibitor bindings to BAZ2A and BAZ2B but also unveils that common residue pairs, including (W1816, W1887), (P1817, P1888), (F1818, F1889), (V1822, V1893), (N1823, N1894),(L1826, L1897), (V1827, V1898), (F1872, F1943), (N1873, N1944) and (V1879, I1950) belonging to (BAZ2A, BAZ2B), induce mainly binding differences of inhibitors to BAZ2A and BAZ2B. Hence, insights from our current studies offer useful dynamics information relating with conformational alterations and structure-affinity relationship at atomistic levels for novel therapeutic strategies toward BAZ2A and BAZ2B.
Collapse
Affiliation(s)
- Lifei Wang
- School
of Science, Shandong Jiaotong University, 5001 Haitang Road, Changqing District, Jinan, Shandong Province 250357, China
| | - Yan Wang
- School
of Science, Shandong Jiaotong University, 5001 Haitang Road, Changqing District, Jinan, Shandong Province 250357, China
| | - Zhiyong Yang
- Department
of Physics, Jiangxi Agricultural University, 1101 Zhimin Road, Economic and Technological
Development Zone, Nanchang, Jiangxi Province 330045, China
| | - Shuobo Xu
- School
of Information Science and Electrical Engineering, Shandong Jiaotong University, 5001 Haitang Road, Changqing District, Jinan, Shandong Province 250357, China
| | - Hongyun Li
- School
of Science, Shandong Jiaotong University, 5001 Haitang Road, Changqing District, Jinan, Shandong Province 250357, China
| |
Collapse
|
11
|
Liu WS, Li HG, Ding CH, Zhang HX, Wang RR, Li JQ. Screening potential FDA-approved inhibitors of the SARS-CoV-2 major protease 3CL pro through high-throughput virtual screening and molecular dynamics simulation. Aging (Albany NY) 2021; 13:6258-6272. [PMID: 33678621 PMCID: PMC7993695 DOI: 10.18632/aging.202703] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 02/03/2021] [Indexed: 04/16/2023]
Abstract
It has been confirmed that the new coronavirus SARS-CoV-2 caused the global pandemic of coronavirus disease 2019 (COVID-19). Studies have found that 3-chymotrypsin-like protease (3CLpro) is an essential enzyme for virus replication, and could be used as a potential target to inhibit SARS-CoV-2. In this work, 3CLpro was used as the target to complete the high-throughput virtual screening of the FDA-approved drugs, and Indinavir and other 10 drugs with high docking scores for 3CLpro were obtained. Studies on the binding pattern of 3CLpro and Indinavir found that Indinavir could form the stable hydrogen bond (H-bond) interactions with the catalytic dyad residues His41-Cys145. Binding free energy study found that Indinavir had high binding affinity with 3CLpro. Subsequently, molecular dynamics simulations were performed on the 3CLpro and 3CLpro-Indinavir systems, respectively. The post-dynamic analyses showed that the conformational state of the 3CLpro-Indinavir system transformed significantly and the system tended to be more stable. Moreover, analyses of the residue interaction network (RIN) and H-bond occupancy revealed that the residue-residue interaction at the catalytic site of 3CLpro was significantly enhanced after binding with Indinavir, which in turn inactivated the protein. In short, through this research, we hope to provide more valuable clues against COVID-19.
Collapse
Affiliation(s)
- Wen-Shan Liu
- Shandong Key Laboratory of Clinical Applied Pharmacology, Department of Pharmacy, Affiliated Hospital of Weifang Medical University, Weifang 261031, Shandong, China
| | - Han-Gao Li
- Shandong Key Laboratory of Clinical Applied Pharmacology, Department of Pharmacy, Affiliated Hospital of Weifang Medical University, Weifang 261031, Shandong, China
| | - Chuan-Hua Ding
- Shandong Key Laboratory of Clinical Applied Pharmacology, Department of Pharmacy, Affiliated Hospital of Weifang Medical University, Weifang 261031, Shandong, China
| | - Hai-Xia Zhang
- Shandong Key Laboratory of Clinical Applied Pharmacology, Department of Pharmacy, Affiliated Hospital of Weifang Medical University, Weifang 261031, Shandong, China
| | - Rui-Rui Wang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin 300070, China
| | - Jia-Qiu Li
- Department of Oncology, Affiliated Hospital of Weifang Medical University, Weifang 261031, Shandong, China
| |
Collapse
|
12
|
Fakhar Z, Khan S, AlOmar SY, Alkhuriji A, Ahmad A. ABBV-744 as a potential inhibitor of SARS-CoV-2 main protease enzyme against COVID-19. Sci Rep 2021; 11:234. [PMID: 33420186 PMCID: PMC7794216 DOI: 10.1038/s41598-020-79918-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 12/01/2020] [Indexed: 01/29/2023] Open
Abstract
A new pathogen severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread worldwide and become pandemic with thousands new deaths and infected cases globally. To address coronavirus disease (COVID-19), currently no effective drug or vaccine is available. This necessity motivated us to explore potential lead compounds by considering drug repurposing approach targeting main protease (Mpro) enzyme of SARS-CoV-2. This enzyme considered to be an attractive drug target as it contributes significantly in mediating viral replication and transcription. Herein, comprehensive computational investigations were performed to identify potential inhibitors of SARS-CoV-2 Mpro enzyme. The structure-based pharmacophore modeling was developed based on the co-crystallized structure of the enzyme with its biological active inhibitor. The generated hypotheses were applied for virtual screening based PhaseScore. Docking based virtual screening workflow was used to generate hit compounds using HTVS, SP and XP based Glide GScore. The pharmacological and physicochemical properties of the selected lead compounds were characterized using ADMET. Molecular dynamics simulations were performed to explore the binding affinities of the considered lead compounds. Binding energies revealed that compound ABBV-744 binds to the Mpro with strong affinity (ΔGbind -45.43 kcal/mol), and the complex is more stable in comparison with other protein-ligand complexes. Our study classified three best compounds which could be considered as promising inhibitors against main protease SARS-CoV-2 virus.
Collapse
Affiliation(s)
- Zeynab Fakhar
- grid.11951.3d0000 0004 1937 1135Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, PO WITS, Johannesburg, 2050 South Africa
| | - Shama Khan
- grid.11951.3d0000 0004 1937 1135Department of Clinical Microbiology and Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 2193 South Africa
| | - Suliman Y. AlOmar
- grid.56302.320000 0004 1773 5396Department of Zoology, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451 Saudi Arabia
| | - Afrah Alkhuriji
- grid.56302.320000 0004 1773 5396Department of Zoology, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451 Saudi Arabia
| | - Aijaz Ahmad
- grid.11951.3d0000 0004 1937 1135Department of Clinical Microbiology and Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 2193 South Africa ,grid.416657.70000 0004 0630 4574Infection Control, Charlotte Maxeke Johannesburg Academic Hospital, National Health Laboratory Service, Johannesburg, 2193 South Africa
| |
Collapse
|
13
|
Elieh Ali Komi D, Shafaghat F, Kovanen PT, Meri S. Mast cells and complement system: Ancient interactions between components of innate immunity. Allergy 2020; 75:2818-2828. [PMID: 32446274 DOI: 10.1111/all.14413] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 04/09/2020] [Accepted: 04/26/2020] [Indexed: 12/23/2022]
Abstract
The emergence and evolution of the complement system and mast cells (MCs) can be traced back to sea urchins and the ascidian Styela plicata, respectively. Acting as a cascade of enzymatic reactions, complement is activated through the classical (CP), the alternative (AP), and the lectin pathway (LP) based on the recognized molecules. The system's main biological functions include lysis, opsonization, and recruitment of phagocytes. MCs, beyond their classic role as master cells of allergic reactions, play a role in other settings, as well. Thus, MCs are considered as extrahepatic producers of complement proteins. They express various complement receptors, including those for C3a and C5a. C3a and C5a not only activate the C3aR and C5aR expressing MCs but also act as chemoattractants for MCs derived from different anatomic sites, such as from the bone marrow, human umbilical cord blood, or skin in vitro. Cross talk between MCs and complement is facilitated by the production of complement proteins by MCs and their activation by the MC tryptase. The coordinated activity between MCs and the complement system plays a key role, for example, in a number of allergic, cutaneous, and vascular diseases. At a molecular level, MCs and complement system interactions are based on the production of several complement zymogens by MCs and their activation by MC-released proteases. Additionally, at a cellular level, MCs act as potent effector cells of complement activation by expressing receptors for C3a and C5a through which their chemoattraction and activation are mediated by anaphylatoxins in a paracrine and autocrine fashion.
Collapse
Affiliation(s)
- Daniel Elieh Ali Komi
- Immunology Research Center Tabriz University of Medical Sciences Tabriz Iran
- Department of Immunology Tabriz University of Medical Sciences Tabriz Iran
| | - Farzaneh Shafaghat
- Immunology Research Center Tabriz University of Medical Sciences Tabriz Iran
- Department of Immunology Tabriz University of Medical Sciences Tabriz Iran
| | | | - Seppo Meri
- Department of Bacteriology and Immunology Immunobiology Research Program University of Helsinki Helsinki Finland
- HUSLAB Helsinki University Central Hospital Helsinki Finland
| |
Collapse
|
14
|
|
15
|
Liu WS, Wang RR, Yue H, Zheng ZH, Lu XH, Wang SQ, Dong WL, Wang RL. Design, synthesis, biological evaluation and molecular dynamics studies of 4-thiazolinone derivatives as protein tyrosine phosphatase 1B (PTP1B) inhibitors. J Biomol Struct Dyn 2019; 38:3814-3824. [PMID: 31490104 DOI: 10.1080/07391102.2019.1664333] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Protein tyrosine phosphatase 1B (PTP1B) is a key negative regulator of insulin signaling pathway, and more and more studies have shown that it is a potential target for the treatment of type 2 diabetes mellitus (T2DM). In this study, 17 new 4-thiazolinone derivatives were designed and synthesized as novel PTP1B inhibitors, and ADMET prediction confirmed that these compounds were to be drug-like. In vitro enzyme activity experiments were performed on these compounds, and it was found that a plurality of compounds had good inhibitory activity and high selectivity against PTP1B protein. Among them, compound 7p exhibited the best inhibitory activity with an IC50 of 0.92 μM. The binding mode of compound 7p and PTP1B protein was explored, revealing the reason for its high efficiency. In addition, molecular dynamics simulations for the PTP1BWT and PTP1Bcomp#7p systems revealed the effects of compound 7p on PTP1B protein at the molecular level. In summary, the study reported for the first time that 4-thiazolinone derivatives as a novel PTP1B inhibitor had good inhibitory activity and selectivity for the treatment of T2DM, providing more options for the development of PTP1B inhibitors. AbbreviationsBBBblood-brain barrierCDC25Bcell division cycle 25 homolog BCYP2D6Cytochrome P450 2D6 bindingDCCMdynamic cross-correlation mapDSDiscovery StudioH bondhydrogen bondHIAhuman intestinal absorptionLARleukocyte antigen-related phosphataseMDmolecular dynamicsMEG-2maternal-effect germ-cell defective 2MM-PBSAmolecular mechanics Poisson Boltzmann surface area)PCAprincipal component analysisPDBProtein Data BankpNPPp-nitrophenyl phosphatePPBplasma protein bindingPTP1Bprotein tyrosine phosphotase 1BRMSDroot mean square deviationRMSFroot mean square fluctuationSHP-1src homologous phosphatase-1SHP-2src homologous phosphatase-2SPCsingle-point chargeTCPTPT cell protein tyrosine phosphataseT2DMType 2 diabetes mellitusVDWvan der WaalsCommunicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Wen-Shan Liu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Rui-Rui Wang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Hai Yue
- Inner Mongolia Institute for Drug Control, Huhhot, Inner Mongolia, China
| | - Zhi-Hui Zheng
- New Drug Research & Development Center of North China Pharmaceutical Group Corporation, National Microbial Medicine Engineering & Research Center, Hebei Industry Microbial Metabolic Engineering & Technology Research Center, Key Laboratory for New Drug Screening Technology of Shijiazhuang City, Shijiazhuang, Hebei, China
| | - Xin-Hua Lu
- New Drug Research & Development Center of North China Pharmaceutical Group Corporation, National Microbial Medicine Engineering & Research Center, Hebei Industry Microbial Metabolic Engineering & Technology Research Center, Key Laboratory for New Drug Screening Technology of Shijiazhuang City, Shijiazhuang, Hebei, China
| | - Shu-Qing Wang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Wei-Li Dong
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Run-Ling Wang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| |
Collapse
|
16
|
Liu WS, Wang RR, Li WY, Rong M, Liu CL, Ma Y, Wang RL. Investigating the reason for loss-of-function of Src homology 2 domain-containing protein tyrosine phosphatase 2 (SHP2) caused by Y279C mutation through molecular dynamics simulation. J Biomol Struct Dyn 2019; 38:2509-2520. [DOI: 10.1080/07391102.2019.1634641] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Wen-Shan Liu
- School of Pharmacy, Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), Tianjin Medical University, Tianjin, China
| | - Rui-Rui Wang
- School of Pharmacy, Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), Tianjin Medical University, Tianjin, China
| | - Wei-Ya Li
- School of Pharmacy, Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), Tianjin Medical University, Tianjin, China
| | - Mei Rong
- School of Pharmacy, Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), Tianjin Medical University, Tianjin, China
| | - Chi-Lu Liu
- School of Pharmacy, Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), Tianjin Medical University, Tianjin, China
| | - Ying Ma
- School of Pharmacy, Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), Tianjin Medical University, Tianjin, China
| | - Run-Ling Wang
- School of Pharmacy, Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), Tianjin Medical University, Tianjin, China
| |
Collapse
|
17
|
Rehman AU, Rafiq H, Rahman MU, Li J, Liu H, Luo S, Arshad T, Wadood A, Chen HF. Gain-of-Function SHP2 E76Q Mutant Rescuing Autoinhibition Mechanism Associated with Juvenile Myelomonocytic Leukemia. J Chem Inf Model 2019; 59:3229-3239. [DOI: 10.1021/acs.jcim.9b00353] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Ashfaq Ur Rehman
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Department of Biochemistry, Abdul Wali Khan University, Mardan 23200, Pakistan
| | - Humaira Rafiq
- Department of Biochemistry, Abdul Wali Khan University, Mardan 23200, Pakistan
| | - Mueed Ur Rahman
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jiayi Li
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hao Liu
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Shenggan Luo
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Taaha Arshad
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Abdul Wadood
- Department of Biochemistry, Abdul Wali Khan University, Mardan 23200, Pakistan
| | - Hai-Feng Chen
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| |
Collapse
|
18
|
Liu WS, Wang RR, Sun YZ, Li WY, Li HL, Liu CL, Ma Y, Wang RL. Exploring the effect of inhibitor AKB-9778 on VE-PTP by molecular docking and molecular dynamics simulation. J Cell Biochem 2019; 120:17015-17029. [PMID: 31125141 DOI: 10.1002/jcb.28963] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 03/03/2019] [Accepted: 03/15/2019] [Indexed: 01/02/2023]
Abstract
Diabetic macular edema, also known as diabetic eye disease, is mainly caused by the overexpression of vascular endothelial protein tyrosine phosphatase (VE-PTP) at hypoxia/ischemic. AKB-9778 is a known VE-PTP inhibitor that can effectively interact with the active site of VE-PTP to inhibit the activity of VE-PTP. However, the binding pattern of VE-PTP with AKB-9778 and the dynamic implications of AKB-9778 on VE-PTP system at the molecular level are poorly understood. Through molecular docking, it was found that the AKB-9778 was docked well in the binding pocket of VE-PTP by the interactions of hydrogen bond and Van der Waals. Furthermore, after molecular dynamic simulations on VE-PTP system and VE-PTP AKB-9778 system, a series of postdynamic analyses found that the flexibility and conformation of the active site undergone an obvious transition after VE-PTP binding with AKB-9778. Moreover, by constructing the RIN, it was found that the different interactions in the active site were the detailed reasons for the conformational differences between these two systems. Thus, the finding here might provide a deeper understanding of AKB-9778 as VE-PTP Inhibitor.
Collapse
Affiliation(s)
- Wen-Shan Liu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Rui-Rui Wang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Ying-Zhan Sun
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Wei-Ya Li
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Hong-Lian Li
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Chi-Lu Liu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Ying Ma
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Run-Ling Wang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| |
Collapse
|
19
|
Wang RR, Liu WS, Zhou L, Ma Y, Wang RL. Probing the acting mode and advantages of RMC-4550 as an Src-homology 2 domain-containing protein tyrosine phosphatase (SHP2) inhibitor at molecular level through molecular docking and molecular dynamics. J Biomol Struct Dyn 2019; 38:1525-1538. [DOI: 10.1080/07391102.2019.1613266] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Rui-Rui Wang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Wen-Shan Liu
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Liang Zhou
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Ying Ma
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Run-Ling Wang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| |
Collapse
|
20
|
Sahu SN, Moharana M, Sahu R, Pattanayak SK. Impact of mutation on podocin protein involved in type 2 nephrotic syndrome: Insights into docking and molecular dynamics simulation study. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.02.120] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
21
|
Wan H, Li J, Chang S, Lin S, Tian Y, Tian X, Wang M, Hu J. Probing the Behaviour of Cas1-Cas2 upon Protospacer Binding in CRISPR-Cas Systems using Molecular Dynamics Simulations. Sci Rep 2019; 9:3188. [PMID: 30816277 PMCID: PMC6395717 DOI: 10.1038/s41598-019-39616-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 01/29/2019] [Indexed: 12/26/2022] Open
Abstract
Adaptation in CRISPR-Cas systems enables the generation of an immunological memory to defend against invading viruses. This process is driven by foreign DNA spacer (termed protospacer) selection and integration mediated by Cas1-Cas2 protein. Recently, different states of Cas1-Cas2, in its free form and in complex with protospacer DNAs, were solved by X-ray crystallography. In this paper, molecular dynamics (MD) simulations are employed to study crystal structures of one free and two protospacer-bound Cas1-Cas2 complexes. The simulated results indicate that the protospacer binding markedly increases the system stability, in particular when the protospacer containing the PAM-complementary sequence. The hydrogen bond and binding free energy calculations explain that PAM recognition introduces more specific interactions to increase the cleavage activity of Cas1. By using principal component analysis (PCA) and intramolecular angle calculation, this study observes two dominant slow motions associated with the binding of Ca1-Cas2 to the protospacer and potential target DNAs respectively. The comparison of DNA structural deformation further implies a cooperative conformational change of Cas1-Cas2 and protospacer for the target DNA capture. We propose that this cooperativity is the intrinsic requirement of the CRISPR integration complex formation. This study provides some new insights into the understanding of CRISPR-Cas adaptation.
Collapse
Affiliation(s)
- Hua Wan
- College of Mathematics and Informatics, South China Agricultural University, Guangzhou, 510642, China
| | - Jianming Li
- College of Mathematics and Informatics, South China Agricultural University, Guangzhou, 510642, China
| | - Shan Chang
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, 213001, China
| | - Shuoxin Lin
- Department of Electrical and Computer Engineering, James Clark School of Engineering, University of Maryland, College Park, MD, 20742, USA
| | - Yuanxin Tian
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Xuhong Tian
- College of Mathematics and Informatics, South China Agricultural University, Guangzhou, 510642, China
| | - Meihua Wang
- College of Mathematics and Informatics, South China Agricultural University, Guangzhou, 510642, China.
| | - Jianping Hu
- College of Pharmacy and Biological Engineering, Sichuan Industrial Institute of Antibiotics, Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Chengdu University, Chengdu, 610106, China.
| |
Collapse
|
22
|
Molecular Dynamics Simulations of Wild Type and Mutants of SAPAP in Complexed with Shank3. Int J Mol Sci 2019; 20:ijms20010224. [PMID: 30626119 PMCID: PMC6337207 DOI: 10.3390/ijms20010224] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Revised: 12/30/2018] [Accepted: 12/30/2018] [Indexed: 01/29/2023] Open
Abstract
Specific interactions between scaffold protein SH3 and multiple ankyrin repeat domains protein 3 (Shank3) and synapse-associated protein 90/postsynaptic density-95–associated protein (SAPAP) are essential for excitatory synapse development and plasticity. In a bunch of human neurological diseases, mutations on Shank3 or SAPAP are detected. To investigate the dynamical and thermodynamic properties of the specific binding between the N-terminal extended PDZ (Post-synaptic density-95/Discs large/Zonaoccludens-1) domain (N-PDZ) of Shank3 and the extended PDZ binding motif (E-PBM) of SAPAP, molecular dynamics simulation approaches were used to study the complex of N-PDZ with wild type and mutated E-PBM peptides. To compare with the experimental data, 974QTRL977 and 966IEIYI970 of E-PBM peptide were mutated to prolines to obtain the M4P and M5P system, respectively. Conformational analysis shows that the canonical PDZ domain is stable while the βN extension presents high flexibility in all systems, especially for M5P. The high flexibility of βN extension seems to set up a barrier for the non-specific binding in this area and provide the basis for specific molecular recognition between Shank3 and SAPAP. The wild type E-PBM tightly binds to N-PDZ during the simulation while loss of binding is observed in different segments of the mutated E-PBM peptides. Energy decomposition and hydrogen bonds analysis show that M4P mutations only disrupt the interactions with canonical PDZ domain, but the interactions with βN1′ remain. In M5P system, although the interactions with βN1′ are abolished, the binding between peptide and the canonical PDZ domain is not affected. The results indicate that the interactions in the two-binding site, the canonical PDZ domain and the βN1′ extension, contribute to the binding between E-PBM and N-PDZ independently. The binding free energies calculated by MM/GBSA (Molecular Mechanics/Generalized Born Surface Area) are in agreement with the experimental binding affinities. Most of the residues on E-PBM contribute considerably favorable energies to the binding except A963 and D964 in the N-terminal. The study provides information to understand the molecular basis of specific binding between Shank3 and SAPAP, as well as clues for design of peptide inhibitors.
Collapse
|
23
|
Probing inhibition mechanisms of adenosine deaminase by using molecular dynamics simulations. PLoS One 2018; 13:e0207234. [PMID: 30444912 PMCID: PMC6239307 DOI: 10.1371/journal.pone.0207234] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 10/27/2018] [Indexed: 02/06/2023] Open
Abstract
Adenosine deaminase (ADA) catalyzes the deamination of adenosine, which is important in purine metabolism. ADA is ubiquitous to almost all human tissues, and ADA abnormalities have been reported in various diseases, including rheumatoid arthritis. ADA can be divided into two conformations based on the inhibitor that it binds to: open and closed forms. Here, we chose three ligands, namely, FR117016 (FR0), FR221647 (FR2) (open form), and HDPR (PRH, closed form), to investigate the inhibition mechanism of ADA and its effect on ADA through molecular dynamics simulations. In open forms, Egap and electrostatic potential (ESP) indicated that electron transfer might occur more easily in FR0 than in FR2. Binding free energy and hydrogen bond occupation revealed that the ADA-FR0 complex had a more stable structure than ADA-FR2. The probability of residues Pro159 to Lys171 of ADA-FR0 and ADA-FR2 to form a helix moderately increased compared with that in nonligated ADA. In comparison with FR0 and FR2 PRH could maintain ADA in a closed form to inhibit the function of ADA. The α7 helix (residues Thr57 to Ala73) of ADA in the closed form was mostly unfastened because of the effect of PRH. The number of H bonds and the relative superiority of the binding free energy indicated that the binding strength of PRH to ADA was significantly lower than that of an open inhibitor, thereby supporting the comparison of the inhibitory activities of the three ligands. Alanine scanning results showed that His17, Gly184, Asp295, and Asp296 exerted the greatest effects on protein energy, suggesting that they played crucial roles in binding to inhibitors. This study served as a theoretical basis for the development of new ADA inhibitors.
Collapse
|
24
|
Sun YZ, Chen XB, Wang RR, Li WY, Ma Y. Exploring the effect of N308D mutation on protein tyrosine phosphatase-2 cause gain-of-function activity by a molecular dynamics study. J Cell Biochem 2018; 120:5949-5961. [PMID: 30304563 DOI: 10.1002/jcb.27883] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 09/19/2018] [Indexed: 01/27/2023]
Abstract
One of the most common protein tyrosine phosphatase-2 (SHP2) mutations in Noonan syndrome is the N308D mutation, and it increases the activity of the protein. However, the molecular basis of the activation of N308D mutation on SHP2 conformations is poorly understood. Here, molecular dynamic simulations were performed on SHP2 and SHP2-N308D to explore the effect of N308D mutation on SHP2 cause gain of function activity, respectively. The principal component analysis, dynamic cross-correlation map, secondary structure analysis, residue interaction networks, and solvent accessible surface area analysis suggested that the N308D mutation distorted the residues interactions network between the allosteric site (residue Gly244-Gly246) and C-SH2 domain, including the hydrogen bond formation and the binding energy. Meanwhile, the activity of catalytic site (residue Gly503-Val505) located in the Q-loop in mutant increased due to this region's high fluctuations. Therefore, the substrate had more chances to access to the catalytic activity site of the precision time protocol domain of SHP2-N308D, which was easy to be exposed. In addition, we had speculated that the Lys244 located in the allosteric site was the key residue which lead to the protein conformation changes. Consequently, overall calculations presented in this study ultimately provide a useful understanding of the increased activity of SHP2 caused by the N308D mutation.
Collapse
Affiliation(s)
- Ying-Zhan Sun
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Xiu-Bo Chen
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China.,Eye Hospital, Tianjin Medical University, School of Optometry and Ophthalmology, Tianjin Medical University, Tianjin, China
| | - Rui-Rui Wang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Wei-Ya Li
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Ying Ma
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| |
Collapse
|
25
|
Prakash A, Kumar V, Meena NK, Hassan MI, Lynn AM. Comparative analysis of thermal unfolding simulations of RNA recognition motifs (RRMs) of TAR DNA-binding protein 43 (TDP-43). J Biomol Struct Dyn 2018; 37:178-194. [DOI: 10.1080/07391102.2017.1422026] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Amresh Prakash
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Vijay Kumar
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Naveen Kumar Meena
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Md. Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Andrew M. Lynn
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| |
Collapse
|
26
|
Li HL, Ma Y, Zheng CJ, Jin WY, Liu WS, Wang RL. Exploring the effect of D61G mutation on SHP2 cause gain of function activity by a molecular dynamics study. J Biomol Struct Dyn 2017; 36:3856-3868. [PMID: 29125030 DOI: 10.1080/07391102.2017.1402709] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Noonan syndrome (NS) is a common autosomal dominant congenital disorder which could cause the congenital cardiopathy and cancer predisposition. Previous studies reported that the knock-in mouse models of the mutant D61G of SHP2 exhibited the major features of NS, which demonstrated that the mutation D61G of SHP2 could cause NS. To explore the effect of D61G mutation on SHP2 and explain the high activity of the mutant, molecular dynamic simulations were performed on wild type (WT) of SHP2 and the mutated SHP2-D61G, respectively. The principal component analysis and dynamic cross-correlation mapping, associated with secondary structure, showed that the D61G mutation affected the motions of two regions (residues Asn 58-Thr 59 and Val 460-His 462) in SHP2 from β to turn. Moreover, the residue interaction networks analysis, the hydrogen bond occupancy analysis and the binding free energies were calculated to gain detailed insight into the influence of the mutant D61G on the two regions, revealing that the major differences between SHP2-WT and SHP2-D61G were the different interactions between Gly 61 and Gly 462, Gly 61 and Ala 461, Gln 506 and Ile 463, Gly 61 and Asn 58, Ile 463 and Thr 466, Gly 462 and Cys 459. Consequently, our findings here may provide knowledge to understand the increased activity of SHP2 caused by the mutant D61G.
Collapse
Key Words
- CHD, congenital heart defects
- D61G
- DCCM, dynamic cross-correlation mapping
- DSPP, Definition of Secondary Structure of Proteins
- H bond, hydrogen bond
- MD, molecular dynamic
- MM-PBSA, molecular mechanics Poisson Boltzmann surface area
- NS, Noonan syndrome
- PCA, principal component analysis
- PTPN11, tyrosine protein phosphatase non-receptor type 11
- RINs, residue interaction networks
- RMSD, root-mean-square deviation
- RMSF, root-mean-square fluctuation
- SH2, Src-homology 2
- SHP2
- SHP2, protein tyrosine phosphatase-2
- SPC, single-point charge
- VDW, Van der Waals
- WT, wild type
- molecular dynamic simulation
Collapse
Affiliation(s)
- Hong-Lian Li
- a Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy , Tianjin Medical University , Tianjin , China
| | - Ying Ma
- a Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy , Tianjin Medical University , Tianjin , China
| | - Chang-Jie Zheng
- a Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy , Tianjin Medical University , Tianjin , China
| | - Wen-Yan Jin
- a Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy , Tianjin Medical University , Tianjin , China
| | - Wen-Shan Liu
- a Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy , Tianjin Medical University , Tianjin , China
| | - Run-Ling Wang
- a Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy , Tianjin Medical University , Tianjin , China
| |
Collapse
|
27
|
Yan F, Liu X, Zhang S, Su J, Zhang Q, Chen J. Computational revelation of binding mechanisms of inhibitors to endocellular protein tyrosine phosphatase 1B using molecular dynamics simulations. J Biomol Struct Dyn 2017; 36:3636-3650. [DOI: 10.1080/07391102.2017.1394221] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Fangfang Yan
- School of Physics and Electronics, Shandong Normal University, Jinan, 250014, China
| | - Xinguo Liu
- School of Physics and Electronics, Shandong Normal University, Jinan, 250014, China
| | - Shaolong Zhang
- School of Physics and Electronics, Shandong Normal University, Jinan, 250014, China
| | - Jing Su
- School of Physics and Electronics, Shandong Normal University, Jinan, 250014, China
| | - Qinggang Zhang
- School of Physics and Electronics, Shandong Normal University, Jinan, 250014, China
| | - Jianzhong Chen
- School of Science, Shandong Jiaotong University, Jinan, 250357, China
| |
Collapse
|
28
|
Prakash A, Dixit G, Meena NK, Singh R, Vishwakarma P, Mishra S, Lynn AM. Elucidation of stable intermediates in urea-induced unfolding pathway of human carbonic anhydrase IX. J Biomol Struct Dyn 2017; 36:2391-2406. [DOI: 10.1080/07391102.2017.1355847] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Amresh Prakash
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Gunjan Dixit
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Naveen Kumar Meena
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Ruhar Singh
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Poonam Vishwakarma
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Smriti Mishra
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Andrew M. Lynn
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| |
Collapse
|
29
|
Kong R, Xu L, Piao L, Zhang D, Hou TJ, Chang S. Exploring the RNA-bound and RNA-free human Argonaute-2 by molecular dynamics simulation method. Chem Biol Drug Des 2017; 90:753-763. [PMID: 28388001 DOI: 10.1111/cbdd.12997] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2017] [Revised: 03/22/2017] [Accepted: 04/03/2017] [Indexed: 01/21/2023]
Abstract
Argonaute 2 (Ago2) protein is the major vehicle of microRNAs (miRNAs)-guided gene repression and silencing processes. Although the crystal structure of human Ago2 (hAgo2) has recently been disclosed, the information of dynamically structural character of protein-RNA recognition is still lacking. Molecular dynamics simulations were used to systematically explore hAgo2 in the presence and absence of RNA duplex. Stable direct and water-mediated hydrogen bonds were observed between guide RNA backbone atoms and hAgo2, especially for nucleotides 2-7. In addition, water-mediated hydrogen bonds are indicated to be critical in the specific recognition between hAgo2 and the conserved adenine in position 1 of target RNA. The core domains (N, PAZ, MID, and PIWI) possess rigid body movements during the simulations. The motions of N-PAZ and PIWI-MID are negatively correlated with or without RNA binding and PAZ domain is identified as the most mobile domain in both systems. The reorientation of PAZ domain not only influences the binding of helix-7 and RNA duplex, the initial pairing process, but also the shape of N-PAZ cleft, where the supplemental base pairing occurs. It is speculated that PAZ domain could be a key regulator in hAgo2-mediated miRNA-induced gene regulation.
Collapse
Affiliation(s)
- Ren Kong
- School of Electrical and Information Engineering, Institute of Bioinformatics and Medical Engineering, Jiangsu University of Technology, Changzhou, China
| | - Lei Xu
- School of Electrical and Information Engineering, Institute of Bioinformatics and Medical Engineering, Jiangsu University of Technology, Changzhou, China
| | - Lianhua Piao
- School of Electrical and Information Engineering, Institute of Bioinformatics and Medical Engineering, Jiangsu University of Technology, Changzhou, China
| | - Dawei Zhang
- School of Electrical and Information Engineering, Institute of Bioinformatics and Medical Engineering, Jiangsu University of Technology, Changzhou, China
| | - Ting-Jun Hou
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Shan Chang
- School of Electrical and Information Engineering, Institute of Bioinformatics and Medical Engineering, Jiangsu University of Technology, Changzhou, China
| |
Collapse
|
30
|
Tian Y, Yu Y, Shen Y, Wan H, Chang S, Zhang T, Wan S, Zhang J. Molecular Simulation Studies on the Binding Selectivity of Type-I Inhibitors in the Complexes with ROS1 versus ALK. J Chem Inf Model 2017; 57:977-987. [PMID: 28318251 DOI: 10.1021/acs.jcim.7b00019] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
ROS1 and ALK are promising targets of anticancer drugs for non-small-cell lung cancer. Since they have 49% amide acid sequence homology in the kinases domain and 77% identity at the ATP binding area, some ALK inhibitors also showed some significant responses for ROS1 in the clinical trial, such as the type-I binding inhibitor crizotinib and PF-06463922. As a newly therapeutic target, the selective ROS1 inhibitor is relatively rare. Moreover, the molecular basis for the selectivity of ROS1 versus ALK still remains unclear. In order to disclose the binding preference toward ROS1 over ALK and to aid the design of selective ROS1 inhibitors, the specific interactions and difference of conformational changes in the dual and selective ROS1/ALK inhibitors systems were investigated by molecular dynamics (MD) simulation and principle component analysis (PCA) in our work. Afterward, binding free energies (MM/GBSA) and binding free energies decomposition analysis indicated that the dominating effect of Van der Waals interaction drives the specific binding process of the type-I inhibitor, and residues of the P-loop and the DFG motif would play an important role in selectivity. On the basis of the modeling results, the new designed compound 14c was verified as a selective ROS1 inhibitor versus ALK, and SMU-B was a dual ROS1/ALK inhibitor by the kinase inhibitory study. These results are expected to facilitate the discovery and rational design of novel and specific ROS1 inhibitors.
Collapse
Affiliation(s)
- Yuanxin Tian
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University , Guangzhou, 510515, People's Republic of China
| | - Yonghuan Yu
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University , Guangzhou, 510515, People's Republic of China
| | - Yudong Shen
- College of Food Sciences, South China Agricultural University , Guangzhou, 510642, People's Republic of China
| | - Hua Wan
- College of Mathematics and Informatics, South China Agricultural University , Guangzhou, 510642, People's Republic of China
| | - Shan Chang
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology , Changzhou, 213001, People's Republic of China
| | - Tingting Zhang
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University , Guangzhou, 510515, People's Republic of China
| | - Shanhe Wan
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University , Guangzhou, 510515, People's Republic of China
| | - Jiajie Zhang
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University , Guangzhou, 510515, People's Republic of China
| |
Collapse
|
31
|
Zhou Y, Zhang N, Chen W, Zhao L, Zhong R. Underlying mechanisms of cyclic peptide inhibitors interrupting the interaction of CK2α/CK2β: comparative molecular dynamics simulation studies. Phys Chem Chem Phys 2017; 18:9202-10. [PMID: 26974875 DOI: 10.1039/c5cp06276d] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Protein-protein interactions (PPIs) are fundamental to all biological processes. Recently, the CK2β-derived cyclic peptide Pc has been demonstrated to efficiently antagonize the CK2α/CK2β interaction and strongly affect the phosphorylation of CK2β-dependent CK2 substrate specificity. The binding affinity of Pc to CK2α is destroyed to different extents by two single-point mutations of Tyr188 to Ala (Y188A) and Phe190 to Ala (F190A), which exert negative effects on the inhibitory activity (IC50) of Pc against the CK2α/CK2β interaction from 3.0 μM to 54.0 μM and ≫100 μM, respectively. However, the structural influences of Y188A and F190A mutations on the CK2α-Pc complex remain unclear. In this study, comparative molecular dynamics (MD) simulations, principal component analysis (PCA), domain cross-correlation map (DCCM) analysis and energy calculations were performed on wild type (WT), Y188A mutant, and F190A mutant systems. The results revealed that ordered communications between hydrophobic and polar interactions were essential for CK2α-Pc binding in the WT system. In addition to the loss of the hydrogen bond between Gln36 of CK2α and Gly189 of Pc in the two mutants, the improper recognition mechanisms occurred through different pathways. These pathways included the weakened hydrophobic interactions in the Y188A mutant as well as decreased polar and hydrophobic interactions in the F190A mutant. The energy analysis results qualitatively elucidated the instability of the two mutants and energetic contributions of the key residues. This study not only revealed the structural mechanisms for the decreased binding affinity of Y188A and F190A mutant CK2α-Pc complexes, but also provided valuable clues for the rational design of CK2α/CK2β subunit interaction inhibitors with high affinity and specificity.
Collapse
Affiliation(s)
- Yue Zhou
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, China.
| | - Na Zhang
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, China.
| | - Wenjuan Chen
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, China.
| | - Lijiao Zhao
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, China.
| | - Rugang Zhong
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, China.
| |
Collapse
|
32
|
Zhao D, Zhou J. Electrostatics-mediated α-chymotrypsin inhibition by functionalized single-walled carbon nanotubes. Phys Chem Chem Phys 2017; 19:986-995. [DOI: 10.1039/c6cp04962a] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Electrostatics-mediated α-chymotrypsin inhibition by functionalized single-walled carbon nanotubes.
Collapse
Affiliation(s)
- Daohui Zhao
- School of Chemistry and Chemical Engineering
- Guangdong Provincial Key Lab for Green Chemical Product Technology
- South China University of Technology
- Guangzhou
- P. R. China
| | - Jian Zhou
- School of Chemistry and Chemical Engineering
- Guangdong Provincial Key Lab for Green Chemical Product Technology
- South China University of Technology
- Guangzhou
- P. R. China
| |
Collapse
|
33
|
Marimuthu P, Singaravelu K, Namasivayam V. Probing the binding mechanism of mercaptoguanine derivatives as inhibitors of HPPK by docking and molecular dynamics simulations. J Biomol Struct Dyn 2016; 35:3507-3521. [PMID: 27844507 DOI: 10.1080/07391102.2016.1260496] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
6-Hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK) is a promising antimicrobial target involved in the folate biosynthesis pathway. Although, the results from crystallographic studies of HPPK have attracted a great interest in the design of novel HPPK inhibitors, the mechanism of action of HPPK due to inhibitor binding remains questionable. Recently, mercaptoguanine derivatives were reported to inhibit the pyrophosphoryl transfer mechanism of Staphylococcus aureus HPPK (SaHPPK). The present study is an attempt to understand the SaHPPK-inhibitors binding mechanism and to highlight the key residues that possibly involve in the complex formation. To decipher these questions, we used the state-of-the-art advanced insilico approach such as molecular docking, molecular dynamics (MD), molecular mechanics-generalized Born surface area approach. Domain cross correlation and principle component analysis were applied to the snapshots obtained from MD revealed that the compounds with high binding affinity stabilize the conformational dynamics of SaHPPK. The binding free energy estimation showed that the van der Waals and electrostatic interactions played a vital role for the binding mechanism. Additionally, the predicted binding free energy was in good agreement with the experimental values (R2 = .78). Moreover, the free energy decomposition on per-residue confirms the key residues that significantly contribute to the complex formation. These results are expected to be useful for rational design of novel SaHPPK inhibitors.
Collapse
Affiliation(s)
- Parthiban Marimuthu
- a Structural Bioinformatics Laboratory (SBL), Faculty of Science and Engineering , Åbo Akademi University , Turku FI-20520 , Finland
| | - Kalaimathy Singaravelu
- b Department of Information Technology, Turku Centre for Biotechnology , University of Turku , Turku FI-20520 , Finland
| | - Vigneshwaran Namasivayam
- c PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Chemistry II , University of Bonn , An der Immenburg 4, Bonn D-53121 , Germany
| |
Collapse
|
34
|
Foster CA, West AH. Use of restrained molecular dynamics to predict the conformations of phosphorylated receiver domains in two-component signaling systems. Proteins 2016; 85:155-176. [PMID: 27802580 PMCID: PMC5242315 DOI: 10.1002/prot.25207] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 10/22/2016] [Accepted: 10/25/2016] [Indexed: 01/22/2023]
Abstract
Two‐component signaling (TCS) is the primary means by which bacteria, as well as certain plants and fungi, respond to external stimuli. Signal transduction involves stimulus‐dependent autophosphorylation of a sensor histidine kinase and phosphoryl transfer to the receiver domain of a downstream response regulator. Phosphorylation acts as an allosteric switch, inducing structural and functional changes in the pathway's components. Due to their transient nature, phosphorylated receiver domains are challenging to characterize structurally. In this work, we provide a methodology for simulating receiver domain phosphorylation to predict conformations that are nearly identical to experimental structures. Using restrained molecular dynamics, phosphorylated conformations of receiver domains can be reliably sampled on nanosecond timescales. These simulations also provide data on conformational dynamics that can be used to identify regions of functional significance related to phosphorylation. We first validated this approach on several well‐characterized receiver domains and then used it to compare the upstream and downstream components of the fungal Sln1 phosphorelay. Our results demonstrate that this technique provides structural insight, obtained in the absence of crystallographic or NMR information, regarding phosphorylation‐induced conformational changes in receiver domains that regulate the output of their associated signaling pathway. To our knowledge, this is the first time such a protocol has been described that can be broadly applied to TCS proteins for predictive purposes. Proteins 2016; 85:155–176. © 2016 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Clay A Foster
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma
| | - Ann H West
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma
| |
Collapse
|
35
|
Chang S, Kong R, Wang LQ, Shi H, Piao LH. Molecular dynamics simulations of wild type and mutant of Pin1 peptidyl-prolyl isomerase. MOLECULAR SIMULATION 2016. [DOI: 10.1080/08927022.2016.1185791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Shan Chang
- School of Electrical and Information Engineering, Institute of Bioinformatics and Medical Engineering, Jiangsu University of Technology, Changzhou, P.R. China
| | - Ren Kong
- School of Electrical and Information Engineering, Institute of Bioinformatics and Medical Engineering, Jiangsu University of Technology, Changzhou, P.R. China
| | - Li-qin Wang
- Changzhou College of Information Technology, Changzhou, P.R. China
| | - Hang Shi
- School of Computer Science & Engineering, Jiangsu University of Technology, Changzhou, P.R. China
| | - Lian-hua Piao
- School of Electrical and Information Engineering, Institute of Bioinformatics and Medical Engineering, Jiangsu University of Technology, Changzhou, P.R. China
| |
Collapse
|
36
|
Zhang Y, Guo J, Li L, Liu X, Yao X, Liu H. The solvent at antigen-binding site regulated C3d–CR2 interactions through the C-terminal tail of C3d at different ion strengths: insights from molecular dynamics simulation. Biochim Biophys Acta Gen Subj 2016; 1860:2220-31. [DOI: 10.1016/j.bbagen.2016.05.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 03/16/2016] [Accepted: 05/02/2016] [Indexed: 12/11/2022]
|
37
|
Decuzzi P. Facilitating the Clinical Integration of Nanomedicines: The Roles of Theoretical and Computational Scientists. ACS NANO 2016; 10:8133-8. [PMID: 27604416 DOI: 10.1021/acsnano.6b05536] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Since the launch of multiple research initiatives on nanotechnology applied to medicine in the early 2000s, a plethora of nanomedicines have been developed that exhibit great therapeutic efficacy in preclinical models but yet minimal impact in daily clinical practice. The successful and complete clinical fruition of nanomedicines requires addressing three major technical challenges: improving loading efficacy and on-command release, modulating recognition and sequestration by immune cells, and maximizing accumulation at biological targets. In this Perspective, I describe how theoretical and computational models can help address each of these challenges. This armamentarium represents an ideal tool for maximizing the therapeutic efficacy of nanomedicines, thus facilitating their integration into daily clinical operations.
Collapse
Affiliation(s)
- Paolo Decuzzi
- Laboratory of Nanotechnology for Precision Medicine, Fondazione Istituto Italiano di Tecnologia Via Morego 30, Genoa 16163, Italy
| |
Collapse
|
38
|
Chang S, Zhang DW, Xu L, Wan H, Hou TJ, Kong R. Exploring the molecular basis of RNA recognition by the dimeric RNA-binding protein via molecular simulation methods. RNA Biol 2016; 13:1133-1143. [PMID: 27592836 DOI: 10.1080/15476286.2016.1223007] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
RNA-binding protein with multiple splicing (RBPMS) is critical for axon guidance, smooth muscle plasticity, and regulation of cancer cell proliferation and migration. Recently, different states of the RNA-recognition motif (RRM) of RBPMS, one in its free form and another in complex with CAC-containing RNA, were determined by X-ray crystallography. In this article, the free RRM domain, its wild type complex and 2 mutant complex systems are studied by molecular dynamics (MD) simulations. Through comparison of free RRM domain and complex systems, it's found that the RNA binding facilitates stabilizing the RNA-binding interface of RRM domain, especially the C-terminal loop. Although both R38Q and T103A/K104A mutations reduce the binding affinity of RRM domain and RNA, the underlining mechanisms are different. Principal component analysis (PCA) and Molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) methods were used to explore the dynamical and recognition mechanisms of RRM domain and RNA. R38Q mutation is positioned on the homodimerization interface and mainly induces the large fluctuations of RRM domains. This mutation does not directly act on the RNA-binding interface, but some interfacial hydrogen bonds are weakened. In contrast, T103A/K104A mutations are located on the RNA-binding interface of RRM domain. These mutations obviously break most of high occupancy hydrogen bonds in the RNA-binding interface. Meanwhile, the key interfacial residues lose their favorable energy contributions upon RNA binding. The ranking of calculated binding energies in 3 complex systems is well consistent with that of experimental binding affinities. These results will be helpful in understanding the RNA recognition mechanisms of RRM domain.
Collapse
Affiliation(s)
- Shan Chang
- a Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology , Changzhou , China
| | - Da-Wei Zhang
- a Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology , Changzhou , China
| | - Lei Xu
- a Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology , Changzhou , China
| | - Hua Wan
- b College of Mathematics and Informatics, South China Agricultural University , Guangzhou , China
| | - Ting-Jun Hou
- c College of Pharmaceutical Sciences, Zhejiang University , Hangzhou , China
| | - Ren Kong
- a Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology , Changzhou , China
| |
Collapse
|
39
|
Metal binding mediated conformational change of XPA protein:a potential cytotoxic mechanism of nickel in the nucleotide excision repair. J Mol Model 2016; 22:156. [PMID: 27307058 DOI: 10.1007/s00894-016-3017-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 05/26/2016] [Indexed: 12/13/2022]
Abstract
Nucleotide excision repair (NER) is a pivotal life process for repairing DNA nucleotide mismatch caused by chemicals, metal ions, radiation, and other factors. As the initiation step of NER, the xeroderma pigmentosum complementation group A protein (XPA) recognizes damaged DNA molecules, and recruits the replication protein A (RPA), another important player in the NER process. The stability of the Zn(2+)-chelated Zn-finger domain of XPA center core portion (i.e., XPA98-210) is the foundation of its biological functionality, while the displacement of the Zn(2+) by toxic metal ions (such as Ni(2+), a known human carcinogen and allergen) may impair the effectiveness of NER and hence elevate the chance of carcinogenesis. In this study, we first calculated the force field parameters for the bonded model in the metal center of the XPA98-210 system, showing that the calculated results, including charges, bonds, angles etc., are congruent with previously reported results measured by spectrometry experiments and quantum chemistry computation. Then, comparative molecular dynamics simulations using these parameters revealed the changes in the conformation and motion mode of XPA98-210 Zn-finger after the substitution of Zn(2+) by Ni(2+). The results showed that Ni(2+) dramatically disrupted the relative positions of the four Cys residues in the Zn-finger structure, forcing them to collapse from a tetrahedron into an almost planar structure. Finally, we acquired the binding mode of XPA98-210 with its ligands RPA70N and DNA based on molecular docking and structural alignment. We found that XPA98-210's Zn-finger domain primarily binds to a V-shaped cleft in RPA70N, while the cationic band in its C-terminal subdomain participates in the recognition of damaged DNA. In addition, this article sheds light on the multi-component interaction pattern among XPA, DNA, and other NER-related proteins (i.e., RPA70N, RPA70A, RPA70B, RPA70C, RPA32, and RPA14) based on previously reported structural biology information. Thus, we derived a putative cytotoxic mechanism associated with the nickel ion, where the Ni(2+) disrupts the conformation of the XPA Zn-finger, directly weakening its interaction with RPA70N, and thus lowering the effectiveness of the NER process. In sum, this work not only provides a theoretical insight into the multi-protein interactions involved in the NER process and potential cytotoxic mechanism associated with Ni(2+) binding in XPA, but may also facilitate rational anti-cancer drug design based on the NER mechanism.
Collapse
|
40
|
Xu L, Kong R, Zhu J, Sun H, Chang S. Unraveling the conformational determinants of LARP7 and 7SK small nuclear RNA by theoretical approaches. MOLECULAR BIOSYSTEMS 2016; 12:2613-21. [DOI: 10.1039/c6mb00252h] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
LARP7, a member of the La-related proteins (LARPs), shares a conserved La module comprising the La-motif (LAM) and the RNA-recognition motif (RRM1), binding exclusively to the non-coding RNA 7SK.
Collapse
Affiliation(s)
- Lei Xu
- Institute of Bioinformatics and Medical Engineering
- School of Electrical and Information Engineering
- Jiangsu University of Technology
- Changzhou 213001
- China
| | - Ren Kong
- Institute of Bioinformatics and Medical Engineering
- School of Electrical and Information Engineering
- Jiangsu University of Technology
- Changzhou 213001
- China
| | - Jingyu Zhu
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou
- China
| | - Huiyong Sun
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou
- China
| | - Shan Chang
- Institute of Bioinformatics and Medical Engineering
- School of Electrical and Information Engineering
- Jiangsu University of Technology
- Changzhou 213001
- China
| |
Collapse
|
41
|
Potential Role of the Last Half Repeat in TAL Effectors Revealed by a Molecular Simulation Study. BIOMED RESEARCH INTERNATIONAL 2016; 2016:8036450. [PMID: 27803930 PMCID: PMC5075638 DOI: 10.1155/2016/8036450] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 08/16/2016] [Accepted: 08/24/2016] [Indexed: 11/30/2022]
Abstract
TAL effectors (TALEs) contain a modular DNA-binding domain that is composed of tandem repeats. In all naturally occurring TALEs, the end of tandem repeats is invariantly a truncated half repeat. To investigate the potential role of the last half repeat in TALEs, we performed comparative molecular dynamics simulations for the crystal structure of DNA-bound TALE AvrBs3 lacking the last half repeat and its modeled structure having the last half repeat. The structural stability analysis indicates that the modeled system is more stable than the nonmodeled system. Based on the principle component analysis, it is found that the AvrBs3 increases its structural compactness in the presence of the last half repeat. The comparison of DNA groove parameters of the two systems implies that the last half repeat also causes the change of DNA major groove binding efficiency. The following calculation of hydrogen bond reveals that, by stabilizing the phosphate binding with DNA at the C-terminus, the last half repeat helps to adopt a compact conformation at the protein-DNA interface. It further mediates more contacts between TAL repeats and DNA nucleotide bases. Finally, we suggest that the last half repeat is required for the high-efficient recognition of DNA by TALE.
Collapse
|
42
|
Molecular dynamics simulation study reveals potential substrate entry path into γ-secretase/presenilin-1. J Struct Biol 2015; 191:120-9. [DOI: 10.1016/j.jsb.2015.07.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Revised: 05/29/2015] [Accepted: 07/01/2015] [Indexed: 11/20/2022]
|
43
|
Chang S, He HQ, Shen L, Wan H. Understanding peptide competitive inhibition of botulinum neurotoxin a binding to SV2 protein via molecular dynamics simulations. Biopolymers 2015; 103:597-608. [DOI: 10.1002/bip.22682] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Revised: 05/09/2015] [Accepted: 05/18/2015] [Indexed: 01/08/2023]
Affiliation(s)
- Shan Chang
- Institute of Bioinformatics and Medical Engineering; School of Electrical and Information Engineering, Jiangsu University of Technology; Changzhou China
| | - Hong-Qiu He
- Chongqing Center for Biomedicines and Medical Equipment; Chongqing Academy of Science and Technology; Chongqing China
| | - Lin Shen
- Institute of Bioinformatics and Medical Engineering; School of Electrical and Information Engineering, Jiangsu University of Technology; Changzhou China
| | - Hua Wan
- College of Informatics; South China Agricultural University; Guangzhou China
| |
Collapse
|
44
|
Wan H, Chang S, Hu JP, Tian YX, Tian XH. Molecular Dynamics Simulations of Ternary Complexes: Comparisons of LEAFY Protein Binding to Different DNA Motifs. J Chem Inf Model 2015; 55:784-94. [PMID: 25734970 DOI: 10.1021/ci500705j] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
LEAFY (LFY) is a plant-specific transcription factor, with a variety of roles in different species. LFY contains a conserved DNA-binding domain (DBD) that determines its DNA-binding specificity. Recently, the structures of the dimeric LFY-DBD bound to different DNA motifs were successively solved by X-ray crystallography. In this article, molecular dynamics (MD) simulations are employed to study two crystal structures of DNA-bound LFY protein from angiosperms and the moss Physcomitrella patens, respectively. The comparison of stabilities of the two systems is consistent with the experimental data of binding affinities. The calculation of hydrogen bonds showed that position 312 in LFY determines the difference of DNA-binding specificity. By using principal component analysis (PCA) and free energy landscape (FEL) methods, the open-close conformational change of the dimerization interface was found to be important for the system stability. At the dimerization interface, the protein-protein interaction has multiple influences on the cooperative DNA binding of LFY. The following analysis of DNA structural parameters further revealed that the protein-protein interaction contributes varying roles according to the specific DNA-binding efficiency. We propose that the protein-protein interaction serves a dual function as a connector between LFY monomers and a regulator of DNA-binding specificity. It will improve the robustness and adaptivity of the LFY-DNA ternary structure. This study provides some new insights into the understanding of the dynamics and interaction mechanism of dimeric LFY-DBD bound to DNA at the atomic level.
Collapse
Affiliation(s)
- Hua Wan
- †College of Informatics, South China Agricultural University, Guangzhou 510642, China
| | - Shan Chang
- ‡Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou 213001, China
| | - Jian-ping Hu
- §Faculty of Biotechnology Industry, Chengdu University, Chengdu 610106, China
| | - Yuan-xin Tian
- ∥School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Xu-hong Tian
- †College of Informatics, South China Agricultural University, Guangzhou 510642, China
| |
Collapse
|
45
|
Bhakat S, Martin AJM, Soliman MES. An integrated molecular dynamics, principal component analysis and residue interaction network approach reveals the impact of M184V mutation on HIV reverse transcriptase resistance to lamivudine. MOLECULAR BIOSYSTEMS 2015; 10:2215-28. [PMID: 24931725 DOI: 10.1039/c4mb00253a] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The emergence of different drug resistant strains of HIV-1 reverse transcriptase (HIV RT) remains of prime interest in relation to viral pathogenesis as well as drug development. Amongst those mutations, M184V was found to cause a complete loss of ligand fitness. In this study, we report the first account of the molecular impact of M184V mutation on HIV RT resistance to 3TC (lamivudine) using an integrated computational approach. This involved molecular dynamics simulation, binding free energy analysis, principle component analysis (PCA) and residue interaction networks (RINs). Results clearly confirmed that M184V mutation leads to steric conflict between 3TC and the beta branched side chain of valine, decreases the ligand (3TC) binding affinity by ∼7 kcal mol(-1) when compared to the wild type, changes the overall conformational landscape of the protein and distorts the native enzyme residue-residue interaction network. The comprehensive molecular insight gained from this study should be of great importance in understanding drug resistance against HIV RT as well as assisting in the design of novel reverse transcriptase inhibitors with high ligand efficacy on resistant strains.
Collapse
Affiliation(s)
- Soumendranath Bhakat
- School of Health Sciences, University of KwaZulu-Natal, Westville, Durban 4001, South Africa.
| | | | | |
Collapse
|
46
|
Wang F, Wan H, Hu JP, Chang S. Molecular dynamics simulations of wild type and mutants of botulinum neurotoxin A complexed with synaptic vesicle protein 2C. MOLECULAR BIOSYSTEMS 2015; 11:223-31. [DOI: 10.1039/c4mb00383g] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Using molecular dynamics simulations, we investigate the relationship between the conformational changes of BoNT/A-RBD:SV2C-LD and the interfacial interactions.
Collapse
Affiliation(s)
- Feng Wang
- School of Information Science & Engineering
- Changzhou University
- Changzhou
- China
| | - Hua Wan
- College of Informatics
- South China Agricultural University
- Guangzhou
- China
| | - Jian-ping Hu
- Faculty of Biotechnology Industry
- Chengdu University
- Chengdu
- China
| | - Shan Chang
- College of Informatics
- South China Agricultural University
- Guangzhou
- China
| |
Collapse
|
47
|
A theoretical view of the C3d:CR2 binding controversy. Mol Immunol 2014; 64:112-22. [PMID: 25433434 DOI: 10.1016/j.molimm.2014.11.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2014] [Accepted: 11/06/2014] [Indexed: 11/23/2022]
Abstract
The C3d:CR2(SCR1-2) interaction plays an important role in bridging innate and adaptive immunity, leading to enhanced antibody production at sites of complement activation. Over the past decade, there has been much debate over the binding mode of this interaction. An initial cocrystal structure (PDB: 1GHQ) was published in 2001, in which the only interactions observed were between the SCR2 domain of CR2 and a side-face of C3d whereas a cocrystal structure (PDB: 3OED) published in 2011 showed both the SCR1 and SCR2 domains of CR2 interacting with an acidic patch on the concave surface of C3d. The initial 1GHQ structure is at odds with the majority of existing biochemical data and the publication of the 3OED structure renewed uncertainty regarding the physiological relevance of 1GHQ, suggesting that crystallization may have been influenced by the presence of zinc acetate in the crystallization process. In our study, we used a variety of computational approaches to gain insight into the binding mode between C3d and CR2 and demonstrate that the binding site at the acidic patch (3OED) is electrostatically more favorable, exhibits better structural and dissociative stability, specifically at the SCR1 domain, and has higher binding affinity than the 1GHQ binding mode. We also observe that nonphysiological zinc ions enhance the formation of the C3d:CR2 complex at the side face of C3d (1GHQ) through increases in electrostatic favorability, intermolecular interactions, dissociative character and overall energetic favorability. These results provide a theoretical basis for the association of C3d:CR2 at the acidic cavity of C3d and provide an explanation for binding of CR2 at the side face of C3d in the presence of nonphysiological zinc ions.
Collapse
|
48
|
Moonsamy S, Bhakat S, Soliman MES. Dynamic features of apo and bound HIV-Nef protein reveal the anti-HIV dimerization inhibition mechanism. J Recept Signal Transduct Res 2014; 35:346-56. [DOI: 10.3109/10799893.2014.984310] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
|
49
|
Wan H, Hu JP, Li KS, Tian XH, Chang S. Molecular dynamics simulations of DNA-free and DNA-bound TAL effectors. PLoS One 2013; 8:e76045. [PMID: 24130757 PMCID: PMC3794935 DOI: 10.1371/journal.pone.0076045] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2013] [Accepted: 08/22/2013] [Indexed: 12/05/2022] Open
Abstract
TAL (transcriptional activator-like) effectors (TALEs) are DNA-binding proteins, containing a modular central domain that recognizes specific DNA sequences. Recently, the crystallographic studies of TALEs revealed the structure of DNA-recognition domain. In this article, molecular dynamics (MD) simulations are employed to study two crystal structures of an 11.5-repeat TALE, in the presence and absence of DNA, respectively. The simulated results indicate that the specific binding of RVDs (repeat-variable diresidues) with DNA leads to the markedly reduced fluctuations of tandem repeats, especially at the two ends. In the DNA-bound TALE system, the base-specific interaction is formed mainly by the residue at position 13 within a TAL repeat. Tandem repeats with weak RVDs are unfavorable for the TALE-DNA binding. These observations are consistent with experimental studies. By using principal component analysis (PCA), the dominant motions are open-close movements between the two ends of the superhelical structure in both DNA-free and DNA-bound TALE systems. The open-close movements are found to be critical for the recognition and binding of TALE-DNA based on the analysis of free energy landscape (FEL). The conformational analysis of DNA indicates that the 5′ end of DNA target sequence has more remarkable structural deformability than the other sites. Meanwhile, the conformational change of DNA is likely associated with the specific interaction of TALE-DNA. We further suggest that the arrangement of N-terminal repeats with strong RVDs may help in the design of efficient TALEs. This study provides some new insights into the understanding of the TALE-DNA recognition mechanism.
Collapse
Affiliation(s)
- Hua Wan
- College of Informatics, South China Agricultural University, Guangzhou, China
| | - Jian-ping Hu
- College of Chemistry, Leshan Normal University, Leshan, China
| | - Kang-shun Li
- College of Informatics, South China Agricultural University, Guangzhou, China
| | - Xu-hong Tian
- College of Informatics, South China Agricultural University, Guangzhou, China
| | - Shan Chang
- College of Informatics, South China Agricultural University, Guangzhou, China
- * E-mail:
| |
Collapse
|