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Mu Y, Meng Q, Fan X, Xi S, Xiong Z, Wang Y, Huang Y, Liu Z. Identification of the inhibition mechanism of carbonic anhydrase II by fructooligosaccharides. Front Mol Biosci 2024; 11:1398603. [PMID: 38863966 PMCID: PMC11165268 DOI: 10.3389/fmolb.2024.1398603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Accepted: 05/06/2024] [Indexed: 06/13/2024] Open
Abstract
Polygonatum sibiricum (P. sibiricum), recognized as a precious nourishing Chinese traditional medicine, exhibits the pharmacological effect of anti-aging. In this work, we proposed a novel mechanism underlying this effect related to the less studied bioactive compounds fructooligosaccharides in P. sibiricum (PFOS) to identify the inhibition effect of the small glycosyl molecules on the age-related zinc metalloprotease carbonic anhydrase II (CA II). Molecular docking and molecular dynamics simulation were used to investigate the structural and energetic properties of the complex systems consisting of the CA II enzyme and two possible structures of PFOS molecules (PFOS-A and PFOS-B). The binding affinity of PFOS-A (-7.27 ± 1.02 kcal/mol) and PFOS-B (-8.09 ± 1.75 kcal/mol) shows the spontaneity of the binding process and the stability of the combination in the solvent. Based on the residue energy decomposition and nonbonded interactions analysis, the C-, D- and G-sheet fragments of the CA II were found to be crucial in binding process. Van der Waals interactions form on the hydrophobic surface of CAII mainly with 131PHE and 135VAL, while hydrogen bonds form on the hydrophilic surface mainly with 67ASN and 92GLN. The binding of PFOS results in the blocking of the zinc ions pocket and then inhibiting its catalytic activity, the stability of which has been further demonstrated by free energy landscape. These findings provide evidence of the effective inhibition of PFOS to CA II enzyme, which leads to a novel direction for exploring the mechanism of traditional Chinese medicine focused on small molecule fructooligosaccharides.
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Affiliation(s)
- Yue Mu
- School of Chemical Engineering, East China University of Science and Technology, Shanghai, China
| | - Qingyang Meng
- Shanghai Pechoin Biotechnology Co., Ltd., Shanghai, China
| | - Xinyi Fan
- Shanghai Pechoin Biotechnology Co., Ltd., Shanghai, China
| | - Shuyun Xi
- Shanghai Pechoin Biotechnology Co., Ltd., Shanghai, China
| | - Zhongli Xiong
- Shanghai Zhengxin Biotechnology Co., Ltd., Shanghai, China
| | - Yihua Wang
- Shanghai Zhengxin Biotechnology Co., Ltd., Shanghai, China
| | - Yanling Huang
- Shanghai Zhengxin Biotechnology Co., Ltd., Shanghai, China
| | - Zhen Liu
- School of Chemical Engineering, East China University of Science and Technology, Shanghai, China
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Zhang Y, Guo J, Liu Y, Qu Y, Li YQ, Mu Y, Li W. An allosteric mechanism for potent inhibition of SARS-CoV-2 main proteinase. Int J Biol Macromol 2024; 265:130644. [PMID: 38462102 DOI: 10.1016/j.ijbiomac.2024.130644] [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: 10/26/2023] [Revised: 02/25/2024] [Accepted: 03/04/2024] [Indexed: 03/12/2024]
Abstract
The main proteinase (Mpro) of SARS-CoV-2 plays a critical role in cleaving viral polyproteins into functional proteins required for viral replication and assembly, making it a prime drug target for COVID-19. It is well known that noncompetitive inhibition offers potential therapeutic options for treating COVID-19, which can effectively reduce the likelihood of cross-reactivity with other proteins and increase the selectivity of the drug. Therefore, the discovery of allosteric sites of Mpro has both scientific and practical significance. In this study, we explored the binding characteristics and inhibiting process of Mpro activity by two recently reported allosteric inhibitors, pelitinib and AT7519 which were obtained by the X-ray screening experiments, to probe the allosteric mechanism via molecular dynamic (MD) simulations. We found that pelitinib and AT7519 can stably bind to Mpro far from the active site. The binding affinity is estimated to be -24.37 ± 4.14 and - 26.96 ± 4.05 kcal/mol for pelitinib and AT7519, respectively, which is considerably stable compared with orthosteric drugs. Furthermore, the strong binding caused clear changes in the catalytic site of Mpro, thus decreasing the substrate accessibility. The community network analysis also validated that pelitinib and AT7519 strengthened intra- and inter-domain communication of Mpro dimer, resulting in a rigid Mpro, which could negatively impact substrate binding. In summary, our findings provide the detailed working mechanism for the two experimentally observed allosteric sites of Mpro. These allosteric sites greatly enhance the 'druggability' of Mpro and represent attractive targets for the development of new Mpro inhibitors.
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Affiliation(s)
- Yunju Zhang
- School of Physics, Shandong University, China
| | - Jingjing Guo
- Centre in Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University, 999078, Macao
| | - Yang Liu
- School of Physics, Shandong University, China
| | - Yuanyuan Qu
- School of Physics, Shandong University, China
| | | | - Yuguang Mu
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
| | - Weifeng Li
- School of Physics, Shandong University, China.
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3
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Zhang Y, Zheng L, Yang Y, Qu Y, Li YQ, Zhao M, Mu Y, Li W. Structural and energetic features of the dimerization of the main proteinase of SARS-CoV-2 using molecular dynamic simulations. Phys Chem Chem Phys 2022; 24:4324-4333. [PMID: 35107451 DOI: 10.1039/d1cp04630f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 has been declared a global health crisis. The development of anti-SARS-CoV-2 drugs heavily depends on the systematic study of the critical biological processes of key proteins of coronavirus among which the main proteinase (Mpro) dimerization is a key step for virus maturation. Because inhibiting the Mpro dimerization can efficiently suppress virus maturation, the key residues that mediate dimerization can be treated as targets of drug and antibody developments. In this work, the structure and energy features of the Mpro dimer of SARS-CoV-2 and SARS-CoV were studied using molecular dynamics (MD) simulations. The free energy calculations using the Generalized Born (GB) model showed that the dimerization free energy of the SARS-CoV-2 Mpro dimer (-107.5 ± 10.89 kcal mol-1) is larger than that of the SARS-CoV Mpro dimer (-92.83 ± 9.81 kcal mol-1), indicating a more stable and possibly a quicker formation of the Mpro dimer of SARS-CoV-2. In addition, the energy decomposition of each residue revealed 11 key attractive residues. Furthermore, Thr285Ala weakens the steric hindrance between the two protomers of SARS-CoV-2 that can form more intimate interactions. It is interesting to find 11 repulsive residues which effectively inhibit the dimerization process. At the interface of the Mpro dimer, we detected three regions that are rich in interfacial water which stabilize the SARS-CoV-2 Mpro dimer by forming hydrogen bonds with two protomers. The key residues and rich water regions provide important targets for the future design of anti-SARS-CoV-2 drugs through inhibiting Mpro dimerization.
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Affiliation(s)
- Yunju Zhang
- School of Physics, Shandong University, Jinan, Shandong, 250100, China
| | | | - Yanmei Yang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University, Jinan, 250014, China
| | - Yuanyuan Qu
- School of Physics, Shandong University, Jinan, Shandong, 250100, China
| | - Yong-Qiang Li
- School of Physics, Shandong University, Jinan, Shandong, 250100, China
| | - Mingwen Zhao
- School of Physics, Shandong University, Jinan, Shandong, 250100, China
| | - Yuguang Mu
- School of Biological Sciences, Nanyang Technological University, Singapore, 637650, Singapore.
| | - Weifeng Li
- School of Physics, Shandong University, Jinan, Shandong, 250100, China.,National Demonstration Center for Experimental Physics Education, Shandong University, China.
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4
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Dráber P, Dráberová E. Dysregulation of Microtubule Nucleating Proteins in Cancer Cells. Cancers (Basel) 2021; 13:cancers13225638. [PMID: 34830792 PMCID: PMC8616210 DOI: 10.3390/cancers13225638] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 11/06/2021] [Accepted: 11/08/2021] [Indexed: 12/12/2022] Open
Abstract
Simple Summary The dysfunction of microtubule nucleation in cancer cells changes the overall cytoskeleton organization and cellular physiology. This review focuses on the dysregulation of the γ-tubulin ring complex (γ-TuRC) proteins that are essential for microtubule nucleation. Recent research on the high-resolution structure of γ-TuRC has brought new insight into the microtubule nucleation mechanism. We discuss the effect of γ-TuRC protein overexpression on cancer cell behavior and new drugs directed to γ-tubulin that may offer a viable alternative to microtubule-targeting agents currently used in cancer chemotherapy. Abstract In cells, microtubules typically nucleate from microtubule organizing centers, such as centrosomes. γ-Tubulin, which forms multiprotein complexes, is essential for nucleation. The γ-tubulin ring complex (γ-TuRC) is an efficient microtubule nucleator that requires additional centrosomal proteins for its activation and targeting. Evidence suggests that there is a dysfunction of centrosomal microtubule nucleation in cancer cells. Despite decades of molecular analysis of γ-TuRC and its interacting factors, the mechanisms of microtubule nucleation in normal and cancer cells remains obscure. Here, we review recent work on the high-resolution structure of γ-TuRC, which brings new insight into the mechanism of microtubule nucleation. We discuss the effects of γ-TuRC protein dysregulation on cancer cell behavior and new compounds targeting γ-tubulin. Drugs inhibiting γ-TuRC functions could represent an alternative to microtubule targeting agents in cancer chemotherapy.
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Wu SL, Zhao J, Sun HB, Li HY, Yin YY, Zhang LL. Insights into interaction mechanism of inhibitors E3T, E3H and E3B with CREB binding protein by using molecular dynamics simulations and MM-GBSA calculations. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2021; 32:221-246. [PMID: 33661069 DOI: 10.1080/1062936x.2021.1887351] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 02/04/2021] [Indexed: 06/12/2023]
Abstract
CREB binding protein (CBP) and its paralog E1A binding protein (p300) are related to the development of inflammatory diseases, cancers and other diseases, and have been potential targets for the treatment of human diseases. In this work, interaction mechanism of three small molecules E3T, E3H, and E3B with CBP was investigated by employing molecular dynamics (MD) simulations, principal component analysis (PCA), and molecular mechanics/generalized born surface area (MM-GBSA) method. The results indicate that inhibitor bindings cause the changes of movement modes and structural flexibility of CBP, and van der Waals interactions mostly drive associations of inhibitors with CBP. In the meantime, the results based on inhibitor-residue interactions not only show that eight residues of CBP can strongly interact with E3T, E3H and E3B but also verify that the CH-CH, CH-π, and π-π interactions are responsible for vital contributions in associations of E3T, E3H and E3B with CBP. In addition, the H-O radial distribution functions (RDFs) were computed to assess the stability of hydrogen bonding interactions between inhibitors and CBP, and the obtained information identifies several key hydrogen bonds playing key roles in bindings of E3T, E3H and E3B to CBP. Potential new inhibitors have been proposed.
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Affiliation(s)
- S L Wu
- School of Science, Shandong Jiaotong University, Jinan, China
| | - J Zhao
- School of Science, Shandong Jiaotong University, Jinan, China
| | - H B Sun
- School of Science, Shandong Jiaotong University, Jinan, China
| | - H Y Li
- School of Science, Shandong Jiaotong University, Jinan, China
| | - Y Y Yin
- School of Science, Shandong Jiaotong University, Jinan, China
| | - L L Zhang
- School of Science, Shandong Jiaotong University, Jinan, China
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6
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Wu SL, Wang LF, Sun HB, Wang W, Yu YX. Probing molecular mechanism of inhibitor bindings to bromodomain-containing protein 4 based on molecular dynamics simulations and principal component analysis. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2020; 31:547-570. [PMID: 32657160 DOI: 10.1080/1062936x.2020.1777584] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 05/31/2020] [Indexed: 06/11/2023]
Abstract
It is well known that bromodomain-containing protein 4 (BRD4) has been thought as a promising target utilized for treating various human diseases, such as inflammatory disorders, malignant tumours, acute myelogenous leukaemia (AML), bone diseases, etc. For this study, molecular dynamics (MD) simulations, binding free energy calculations, and principal component analysis (PCA) were integrated together to uncover binding modes of inhibitors 8P9, 8PU, and 8PX to BRD4(1). The results obtained from binding free energy calculations show that van der Waals interactions act as the main regulator in bindings of inhibitors to BRD4(1). The information stemming from PCA reveals that inhibitor associations extremely affect conformational changes, internal dynamics, and movement patterns of BRD4(1). Residue-based free energy decomposition method was wielded to unveil contributions of independent residues to inhibitor bindings and the data signify that hydrogen bonding interactions and hydrophobic interactions are decisive factors affecting bindings of inhibitors to BRD4(1). Meanwhile, eight residues Trp81, Pro82, Val87, Leu92, Leu94, Cys136, Asn140, and Ile146 are recognized as the common hot interaction spots of three inhibitors with BRD4(1). The results from this work are expected to provide a meaningfully theoretical guidance for design and development of effective inhibitors inhibiting of the activity of BRD4.
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Affiliation(s)
- S L Wu
- School of Science, Shandong Jiaotong University , Jinan, China
| | - L F Wang
- School of Science, Shandong Jiaotong University , Jinan, China
| | - H B Sun
- School of Science, Shandong Jiaotong University , Jinan, China
| | - W Wang
- School of Science, Shandong Jiaotong University , Jinan, China
| | - Y X Yu
- School of Science, Shandong Jiaotong University , Jinan, China
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7
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Wang Y, Wang LF, Zhang LL, Sun HB, Zhao J. Molecular mechanism of inhibitor bindings to bromodomain-containing protein 9 explored based on molecular dynamics simulations and calculations of binding free energies. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2020; 31:149-170. [PMID: 31851834 DOI: 10.1080/1062936x.2019.1701075] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 12/02/2019] [Indexed: 06/10/2023]
Abstract
Recently, bromodomain-containing protein 9 (BRD9) has been a prospective therapeutic target for anticancer drug design. Molecular dynamics (MD) simulations combined with molecular mechanics generalized Born surface area (MM-GBSA) method were adopted to explore binding modes of three inhibitors (5SW, 5U2, and 5U6) to BRD9 and identify the hot spot of the inhibitor-BRD9 binding. The results indicate that the inhibitor 5SW has the strongest binding ability to BRD9 among the current three inhibitors. Furthermore, the rank of the binding free energies predicted by MM-GBSA approach agrees with that determined by the experimental values. In addition, inhibitor-residue interactions were computed by using residue-based free-energy decomposition method and the results suggest that residue His42 produces the CH-H interactions, residues Asn100, Ile53 and Val49 produce the CH-[Formula: see text] interactions with three inhibitors and Tyr106, Phe45 and Phe44 generate the π-π interactions with inhibitors. Notably, the residue Asn140 forms hydrogen bonding interactions with three inhibitors. This research is expected to provide useful molecular basis and dynamics information at atomic levels for the design of potent inhibitors inhibiting the activity of BRD9.
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Affiliation(s)
- Y Wang
- School of Science, Shandong Jiaotong University, Jinan, China
| | - L F Wang
- School of Science, Shandong Jiaotong University, Jinan, China
| | - L L Zhang
- School of Science, Shandong Jiaotong University, Jinan, China
| | - H B Sun
- School of Science, Shandong Jiaotong University, Jinan, China
| | - J Zhao
- School of Science, Shandong Jiaotong University, Jinan, China
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8
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Chahal V, Nirwan S, Kakkar R. Combined approach of homology modeling, molecular dynamics, and docking: computer-aided drug discovery. PHYSICAL SCIENCES REVIEWS 2019. [DOI: 10.1515/psr-2019-0066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
With the continuous development in software, algorithms, and increase in computer speed, the field of computer-aided drug design has been witnessing reduction in the time and cost of the drug designing process. Structure based drug design (SBDD), which is based on the 3D structure of the enzyme, is helping in proposing novel inhibitors. Although a number of crystal structures are available in various repositories, there are various proteins whose experimental crystallization is difficult. In such cases, homology modeling, along with the combined application of MD and docking, helps in establishing a reliable 3D structure that can be used for SBDD. In this review, we have reported recent works, which have employed these three techniques for generating structures and further proposing novel inhibitors, for cytoplasmic proteins, membrane proteins, and metal containing proteins. Also, we have discussed these techniques in brief in terms of the theory involved and the various software employed. Hence, this review can give a brief idea about using these tools specifically for a particular problem.
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9
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Altinoz MA, Topcu G, Hacimuftuoglu A, Ozpinar A, Ozpinar A, Hacker E, Elmaci İ. Noscapine, a Non-addictive Opioid and Microtubule-Inhibitor in Potential Treatment of Glioblastoma. Neurochem Res 2019; 44:1796-1806. [PMID: 31292803 DOI: 10.1007/s11064-019-02837-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 06/12/2019] [Accepted: 06/21/2019] [Indexed: 02/08/2023]
Abstract
Noscapine is a phthalide isoquinoline alkaloid that easily traverses the blood brain barrier and has been used for years as an antitussive agent with high safety. Despite binding opioid receptors, noscapine lacks significant hypnotic and euphoric effects rendering it safe in terms of addictive potential. In 1954, Hans Lettré first described noscapine as a mitotic poison. The drug was later tested for cancer treatment in the early 1960's, yet no effect was observed likely as a result of its short biological half-life and limited water solubility. Since 1998, it has regained interest thanks to studies from Emory University, which showed its anticancer activity in animal models with negligible toxicity. In contrast to other microtubule-inhibitors, noscapine does not affect the total intracellular tubulin polymer mass. Instead, it forces the microtubules to spend an increased amount of time in a paused state leading to arrest in mitosis and subsequently inducing mitotic slippage/mitotic catastrophe/apoptosis. In experimental models, noscapine does not induce peripheral neuropathy, which is common with other microtubule inhibitors. Noscapine also inhibits tumor growth and enhances cancer chemosensitivity via selective blockage of NF-κB, an important transcription factor in glioblastoma pathogenesis. Due to their anticancer activities and high penetration through the blood-brain barrier, noscapine analogues strongly deserve further study in various animal models of glioblastoma as potential candidates for future patient therapy.
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Affiliation(s)
- Meric A Altinoz
- Department of Medical Biochemistry, Acibadem University, Istanbul, Turkey. .,Department of Psychiatry, Maastricht University, Maastricht, The Netherlands.
| | - Gulacti Topcu
- Department of Pharmacy, Bezmi Alem University, Istanbul, Turkey
| | - Ahmet Hacimuftuoglu
- Department of Medical Pharmacology, Erzurum Ataturk University, Erzurum, Turkey
| | - Alp Ozpinar
- Department of Neurosurgery, University of Pittsburgh, Pittsburgh, USA
| | - Aysel Ozpinar
- Department of Medical Biochemistry, Acibadem University, Istanbul, Turkey
| | - Emily Hacker
- Department of Neurosurgery, University of Pittsburgh, Pittsburgh, USA
| | - İlhan Elmaci
- Department of Neurosurgery, Acibadem Hospital, Istanbul, Turkey
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Pradhan S, Sarma H, Mattaparthi VSK. Investigation of the probable homo-dimer model of the Xeroderma pigmentosum complementation group A (XPA) protein to represent the DNA-binding core. J Biomol Struct Dyn 2018; 37:3322-3336. [PMID: 30205752 DOI: 10.1080/07391102.2018.1517051] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The Xeroderma pigmentosum complementation group A (XPA) protein functions as a primary damage verifier and as a scaffold protein in nucleotide excision repair (NER) in all higher organisms. New evidence of XPA's existence as a dimer and the redefinition of its DNA-binding domain (DBD) raises new questions regarding the stability and functional position of XPA in NER. Here, we have investigated XPA's dimeric status with respect to its previously defined DBD (XPA98-219) as well as with its redefined DBD (XPA98-239). We studied the stability of XPA98-210 and XPA98-239 homo-dimer systems using all-atom molecular dynamics simulation, and we have also characterized the protein-protein interactions (PPI) of these two homo-dimeric forms of XPA. After conducting the root mean square deviation (RMSD) analyses, it was observed that the XPA98-239 homo-dimer has better stability than XPA98-210. It was also found that XPA98-239 has a larger number of hydrogen bonds, salt bridges, and hydrophobic interactions than the XPA98-210 homo-dimer. We further found that Lys, Glu, Gln, Asn, and Arg residues shared the major contribution toward the intermolecular interactions in XPA homo-dimers. The binding free energy (BFE) analysis, which used the molecular mechanics Poisson-Boltzmann method (MM-PBSA) and the generalized Born and surface area continuum solvation model (GBSA) for both XPA homo-dimers, also substantiated the positive result in favor of the stability of the XPA98-239 homo-dimer. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sushmita Pradhan
- a Molecular Modelling and Simulation Laboratory, Department of Molecular Biology and Biotechnology , Tezpur University , Tezpur , India
| | - Himakshi Sarma
- a Molecular Modelling and Simulation Laboratory, Department of Molecular Biology and Biotechnology , Tezpur University , Tezpur , India
| | - Venkata Satish Kumar Mattaparthi
- a Molecular Modelling and Simulation Laboratory, Department of Molecular Biology and Biotechnology , Tezpur University , Tezpur , India
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Zúñiga MA, Alderete JB, Jaña GA, Fernandez PA, Ramos MJ, Jiménez VA. Modulation of lateral and longitudinal interdimeric interactions in microtubule models by Laulimalide and Peloruside A association: A molecular modeling approach on the mechanism of microtubule stabilizing agents. Chem Biol Drug Des 2018; 91:1042-1055. [DOI: 10.1111/cbdd.13168] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 12/27/2017] [Accepted: 12/31/2017] [Indexed: 01/10/2023]
Affiliation(s)
- Matías A. Zúñiga
- Departamento de Ciencias Químicas; Facultad de Ciencias Exactas; Universidad Andres Bello; Talcahuano Chile
| | - Joel B. Alderete
- Departamento de Química Orgánica; Facultad de Ciencias Químicas; Universidad de Concepción; Concepción Chile
| | - Gonzalo A. Jaña
- Departamento de Ciencias Químicas; Facultad de Ciencias Exactas; Universidad Andres Bello; Talcahuano Chile
| | | | - Maria J. Ramos
- Faculdade de Ciencias; Universidad do Porto; Porto Portugal
| | - Verónica A. Jiménez
- Departamento de Ciencias Químicas; Facultad de Ciencias Exactas; Universidad Andres Bello; Talcahuano Chile
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12
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Wang C, Greene D, Xiao L, Qi R, Luo R. Recent Developments and Applications of the MMPBSA Method. Front Mol Biosci 2018; 4:87. [PMID: 29367919 PMCID: PMC5768160 DOI: 10.3389/fmolb.2017.00087] [Citation(s) in RCA: 332] [Impact Index Per Article: 55.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 11/30/2017] [Indexed: 12/23/2022] Open
Abstract
The Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) approach has been widely applied as an efficient and reliable free energy simulation method to model molecular recognition, such as for protein-ligand binding interactions. In this review, we focus on recent developments and applications of the MMPBSA method. The methodology review covers solvation terms, the entropy term, extensions to membrane proteins and high-speed screening, and new automation toolkits. Recent applications in various important biomedical and chemical fields are also reviewed. We conclude with a few future directions aimed at making MMPBSA a more robust and efficient method.
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Affiliation(s)
- Changhao Wang
- Chemical and Materials Physics Graduate Program, University of California, Irvine, Irvine, CA, United States
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
- Department of Physics and Astronomy, University of California, Irvine, Irvine, CA, United States
| | - D'Artagnan Greene
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
| | - Li Xiao
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, United States
| | - Ruxi Qi
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
| | - Ray Luo
- Chemical and Materials Physics Graduate Program, University of California, Irvine, Irvine, CA, United States
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, United States
- Department of Chemical Engineering and Materials Science, University of California, Irvine, Irvine, CA, United States
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13
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Ghaly PE, Churchill CD, Abou El-Magd RM, Hájková Z, Dráber P, West F, Tuszynski JA. Synthesis and biological evaluation of structurally simplified noscapine analogues as microtubule binding agents. CAN J CHEM 2017. [DOI: 10.1139/cjc-2016-0649] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
This paper reports on the results of chemical synthesis and biological assays performed on several new analogues of noscapine. We have successfully synthesized four noscapine analogues called 1a–4a, as well as their four corresponding enantiomers called 1b–4b. The chemical pathway consisted of three steps with yields in excess of 60% in each step. Subsequently, we have performed biological activity assays intended to reveal the mode of action of these compounds on microtubules in buffer and in cancer cell lines. We have assayed fluorescence quenching effects in microtubule polymerization experiments, cytotoxicity evaluation in breast cancer cell lines, as well as microtubule dynamicity assessments, for each of the synthesized compounds. Finally, we performed computational docking simulations to two binding sites on β-tubulin: (a) the colchicine binding site and (b) the noscapine binding site. Our results indicate that these compounds have relatively low cytotoxicity profile and less pronounced effects on microtubule dynamics compared with noscapine. Our computational results indicate that these compounds bind to both putative binding sites but have higher affinity for the colchicine site.
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Affiliation(s)
- Peter E. Ghaly
- Department of Chemistry, University of Alberta, E3-43 Gunning-Lemieux Chemistry Center, Edmonton, AB T6G 2G2, Canada
| | - Cassandra D.M. Churchill
- Department of Chemistry, University of Alberta, E3-43 Gunning-Lemieux Chemistry Center, Edmonton, AB T6G 2G2, Canada
| | - Rabab M. Abou El-Magd
- Department of Oncology, University of Alberta, Edmonton, AB T6G 1Z2, Canada
- Genetic Engineering and Biotechnology Institute, City of Scientific Research and Technological Application, New Borg El-Arab City, Alexandria, 21934, Egypt
| | - Zuzana Hájková
- Laboratory of Biology of Cytoskeleton, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, CZ-142 20, Prague 4, Czech Republic
| | - Pavel Dráber
- Laboratory of Biology of Cytoskeleton, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, CZ-142 20, Prague 4, Czech Republic
| | - F.G. West
- Department of Chemistry, University of Alberta, E3-43 Gunning-Lemieux Chemistry Center, Edmonton, AB T6G 2G2, Canada
| | - Jack A. Tuszynski
- Department of Oncology, University of Alberta, Edmonton, AB T6G 1Z2, Canada
- Department of Physics, University of Alberta, Edmonton, AB T6G 2E1, Canada
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14
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Zarei O, Hamzeh-Mivehroud M, Benvenuti S, Ustun-Alkan F, Dastmalchi S. Characterizing the Hot Spots Involved in RON-MSPβ Complex Formation Using In Silico Alanine Scanning Mutagenesis and Molecular Dynamics Simulation. Adv Pharm Bull 2017; 7:141-150. [PMID: 28507948 PMCID: PMC5426727 DOI: 10.15171/apb.2017.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 03/18/2017] [Accepted: 03/20/2017] [Indexed: 12/30/2022] Open
Abstract
Purpose: Implication of protein-protein interactions (PPIs) in development of many diseases such as cancer makes them attractive for therapeutic intervention and rational drug design. RON (Recepteur d'Origine Nantais) tyrosine kinase receptor has gained considerable attention as promising target in cancer therapy. The activation of RON via its ligand, macrophage stimulation protein (MSP) is the most common mechanism of activation for this receptor. The aim of the current study was to perform in silico alanine scanning mutagenesis and to calculate binding energy for prediction of hot spots in protein-protein interface between RON and MSPβ chain (MSPβ). Methods: In this work the residues at the interface of RON-MSPβ complex were mutated to alanine and then molecular dynamics simulation was used to calculate binding free energy. Results: The results revealed that Gln193, Arg220, Glu287, Pro288, Glu289, and His424 residues from RON and Arg521, His528, Ser565, Glu658, and Arg683 from MSPβ may play important roles in protein-protein interaction between RON and MSP. Conclusion: Identification of these RON hot spots is important in designing anti-RON drugs when the aim is to disrupt RON-MSP interaction. In the same way, the acquired information regarding the critical amino acids of MSPβ can be used in the process of rational drug design for developing MSP antagonizing agents, the development of novel MSP mimicking peptides where inhibition of RON activation is required, and the design of experimental site directed mutagenesis studies.
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Affiliation(s)
- Omid Zarei
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran.,Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Students Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Maryam Hamzeh-Mivehroud
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Medicinal Chemistry, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Silvia Benvenuti
- Molecular Therapeutics and Exploratory Research Laboratory, Candiolo Cancer Institute-FPO-IRCCS, Candiolo, Turin, Italy
| | - Fulya Ustun-Alkan
- Department of Pharmacology and Toxicology, Faculty of Veterinary Medicine, Istanbul University, Istanbul, Turkey
| | - Siavoush Dastmalchi
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Medicinal Chemistry, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
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15
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Sirtuin 5: a review of structure, known inhibitors and clues for developing new inhibitors. SCIENCE CHINA-LIFE SCIENCES 2016; 60:249-256. [DOI: 10.1007/s11427-016-0060-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 05/23/2016] [Indexed: 12/31/2022]
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16
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Characterization of Promiscuous Binding of Phosphor Ligands to Breast-Cancer-Gene 1 (BRCA1) C-Terminal (BRCT): Molecular Dynamics, Free Energy, Entropy and Inhibitor Design. PLoS Comput Biol 2016; 12:e1005057. [PMID: 27560145 PMCID: PMC4999267 DOI: 10.1371/journal.pcbi.1005057] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 07/07/2016] [Indexed: 01/17/2023] Open
Abstract
Inhibition of the protein-protein interaction (PPI) mediated by breast-cancer-gene 1 C-terminal (BRCT) is an attractive strategy to sensitize breast and ovarian cancers to chemotherapeutic agents that induce DNA damage. Such inhibitors could also be used for studies to understand the role of this PPI in DNA damage response. However, design of BRCT inhibitors is challenging because of the inherent flexibility associated with this domain. Several studies identified short phosphopeptides as tight BRCT binders. Here we investigated the thermodynamic properties of 18 phosphopeptides or peptide with phosphate mimic and three compounds with phosphate groups binding to BRCT to understand promiscuous molecular recognition and guide inhibitor design. We performed molecular dynamics (MD) simulations to investigate the interactions between inhibitors and BRCT and their dynamic behavior in the free and bound states. MD simulations revealed the key role of loops in altering the shape and size of the binding site to fit various ligands. The mining minima (M2) method was used for calculating binding free energy to explore the driving forces and the fine balance between configuration entropy loss and enthalpy gain. We designed a rigidified ligand, which showed unfavorable experimental binding affinity due to weakened enthalpy. This was because it lacked the ability to rearrange itself upon binding. Investigation of another phosphate group containing compound, C1, suggested that the entropy loss can be reduced by preventing significant narrowing of the energy well and introducing multiple new compound conformations in the bound states. From our computations, we designed an analog of C1 that introduced new intermolecular interactions to strengthen attractions while maintaining small entropic penalty. This study shows that flexible compounds do not always encounter larger entropy penalty, compared with other more rigid binders, and highlights a new strategy for inhibitor design. Promiscuous proteins are commonly observed in biological systems, such as modular domains that recognize phosphopeptides during signal transduction. The use of phosphopeptides and compounds with phosphate groups as inhibitors to protein–protein interactions have attracted increasing interest for years. By using atomistic molecular dynamics simulations, we are able to perform detailed analyses of the dihedral space to explore protein fluctuation upon ligand binding to better understand promiscuous molecular recognition. Free energy calculation can further provide insights into the mechanism of binding, including both enthalpic and entropic contributions for molecular recognition, which assist in inhibitor design. Our calculation results show that pre-rigidifying a ligand is not always advantageous, suggesting the challenge in retaining optimized intermolecular interactions in pre-rigidified ligand. Instead, certain flexible ligands with multiple binding conformations can reduce entropic penalty, and therefore improves binding affinity. According to our computations, we can introduce new intermolecular interactions to flexible ligand to strengthen attractions while maintaining small entropic penalty by retaining its plasticity in the bound conformation. The study might cast light on a new general strategy for designing inhibitors targeting promiscuous modular domains and protein–protein interactions.
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