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Journal of Molecular Graphics & Modelling

Baban S Kolte, Sanjay R Londhe, Bhushan R Solanki, Rajesh N Gacche, Rohan J Meshram
Finding novel chemical agents for targeting disease associated drug targets often requires screening of large number of new chemical libraries. In silico methods are generally implemented at initial stages for virtual screening. Filtering of such compound libraries on physicochemical and substructure ground is done to ensure elimination of compounds with undesired chemical properties. Filtering procedure, is redundant, time consuming and requires efficient bioinformatics/computer manpower along with high end software involving huge capital investment that forms a major obstacle in drug discovery projects in academic setup...
January 6, 2018: Journal of Molecular Graphics & Modelling
S Hooman Vahidi, Mohammad Reza Bozorgmehr, Ali Morsali, S Ali Beyramabadi
Studies have shown that deletion of amino acids from the C-terminus of amylase do not alter its amylolytic activity. Although high pressure is used to modify the structure and function of this enzyme, the effects of high pressures on the structures of the wild-type and truncated amylases have not yet been understood at the molecular level. Using molecular dynamic simulations and docking, we studied the structures of wild-type and truncated Taka-amylases at high pressures (1000-4000 bar). To construct the truncated Taka-amylase, 50 and 100 C-terminal residues were removed in two separate steps...
January 6, 2018: Journal of Molecular Graphics & Modelling
Zhengyan Zhao, Xuedan Song, Lei Liu, Guanglan Li, Shaheen Shah, Ce Hao
This article presents a recognition mechanism for nitro-explosives by the luminescent metal-organic framework 1 (LMOF-1) with the aid of density functional theory (DFT) and time-dependent density functional theory (TDDFT). The behavior of hydrogen bonding between the LMOF-1 and nitro-explosives in the S1 state is closely associated with the fluorescence properties of the LMOF-1. In our research, we calculated the geometric configuration, 1H NMR and IR spectra of the Complex 2 formed by LMOF-1 and nitrobenzene in the S0 and S1 states...
January 5, 2018: Journal of Molecular Graphics & Modelling
Baohe Wang, Yan Nie, Jing Ma
Combing molecular dynamics (MD) and Grand Canonical Monte Carlo (GCMC) simulation, the effect of bioadhesive transition layer on the interfacial compatibility of the pervaporation composite membranes, and the pervaporation performance toward penetrant molecules were investigated. In our previous experimental study, the structural stability and permeability selectivity of the composite membranes were considerably enhanced by the introduction of bioadhesive carbopol (CP). In the present study, the interfacial compatibility and the interfacial energies between the chitosan (CS) separation layer, CP transition layer and the support layer were investigated, respectively...
January 5, 2018: Journal of Molecular Graphics & Modelling
Younes Valadbeigi
Aromaticities and stabilities of ortho, meta, and para isomers of some derivatives of benzene, C5H5- and C7H7+ were studied and compared basis on the NICS index and their relative energies. For the benzene and C7H7+ derivatives, the ortho isomers with less stability were more aromatic. This discrepancy was also observed for the molecules with conjugated and non-conjugated π-electrons. However, for the charged conjugated systems, the structures with delocalized charge were more stable. Effect of electron withdrawing (EWGs) and electron donating groups (EDGs) on the electron delocalization and stability of the neutral and charged molecules was investigated...
January 5, 2018: Journal of Molecular Graphics & Modelling
Farhad Jahanfar, Hamed Hamishehkar
The polymorphism rs10490924 (A69S) in the age-related maculopathy susceptibility 2 (ARMS2) gene is highly associated with age-related macular degeneration, which is the leading cause of blindness among the elderly population. ARMS2 gene encodes a putative small (11 kDa) protein, which the function and localization of the ARMS2 protein remain under debate. For a better understanding of functional impacts of A69S mutation, we performed a detailed analysis of an ARMS2 sequence with a broad set of bioinformatics tools...
January 4, 2018: Journal of Molecular Graphics & Modelling
Mehdi D Esrafili, Leila Dinparast
Density functional theory (DFT) calculations are performed to study the adsorption behavior of formaldehyde and methanol on the pristine as well as Al- or Si-decorated graphene oxide (GO). The most stable adsorption configurations, adsorption energies, binding distances and net charge transfers are obtained to understand the impacts of the these molecules on the electronic properties of the pristine or metal-decorated GO surface. The pristine GO exhibits a low sensitivity to both formaldehyde and methanol molecules...
January 2, 2018: Journal of Molecular Graphics & Modelling
Yinguang Zhang, Yongwang Zhang, Yuxiang Zhang
Human sacum is regulatory adaptor protein involved in cellular signaling network of colorectal cancer. Molecular evidences suggest that the protein is integrated into oncogenic signaling network by binding to SH3-containing proteins through its proline-rich motifs. In this study, we have performed a transcriptome-wide analysis and identification of sacum-binding partners in the genome profile of human colorectal cancer. The sacum-binding potency of SH3-containing proteins found in colorectal cancer was investigated by using bioinformatics modeling and intermolecular binding analysis...
December 30, 2017: Journal of Molecular Graphics & Modelling
Jason S E Loo, Abigail L Emtage, Kar Weng Ng, Alene S J Yong, Stephen W Doughty
GPCR crystal structures have become more readily accessible in recent years. However, homology models of GPCRs continue to play an important role as many GPCR structures remain unsolved. The new crystal structures now available provide not only additional templates for homology modelling but also the opportunity to assess the performance of homology models against their respective crystal structures and gain insight into the performance of such models. In this study we have constructed homology models from templates of various transmembrane sequence identities for eight GPCR targets to better understand the relationship between transmembrane sequence identity and model quality...
December 29, 2017: Journal of Molecular Graphics & Modelling
Mahshid Hamzehloueian, Zakieh Davari
The molecular mechanism of the [3+2] cycloaddition (32CA) reaction of an azomethine ylide, generated in situ from isatin and sarcosine, with benzo-imidazol-2-yl-3-phenylacrylonitrile have been theoretically studied by using DFT at the B3LYP and M06-2X levels of theory. This reaction takes place through an asynchronous one-step mechanism. Analysis of the global electron density transfer (GEDT) indicates that this 32CA has a polar character. The regiochemistry of this reaction was investigated using Parr functions analysis, as well as HSAB principle and potential energy surface analysis, where the results are in agreement with the experimental observations...
December 29, 2017: Journal of Molecular Graphics & Modelling
Dušan Ž Veljković
Energies of CH/O interactions between water molecule and polycyclic aromatic hydrocarbons with a different number of aromatic rings were calculated using ab initio calculations at MP2/cc-PVTZ level. Results show that an additional aromatic ring in structure of polycyclic aromatic hydrocarbons significantly strengthens CH/O interactions. Calculated interaction energies in optimized structures of the most stable tetracene/water complex is -2.27 kcal/mol, anthracene/water is -2.13 kcal/mol and naphthalene/water is -1...
December 28, 2017: Journal of Molecular Graphics & Modelling
Joel A Olson, Raymond J Terryn, Elizabeth L Stewart, J Clayton Baum, Mark J Novak
A new submolecular quantitative structure activity relationship (QSAR) descriptor was applied toward elucidating the anti-malarial pharmacophore of tryptanthrins, a class of compounds known for their anti-parasitic activities. The new descriptor is based on experimental and computational measurements of the tunneling barriers of individual lobes of the molecular orbitals. Lobe-by-lobe QSAR correlation plots revealed a single lobe of the LUMO to be strongly associated with tryptanthrin's anti-malarial activity...
December 27, 2017: Journal of Molecular Graphics & Modelling
Nouman Rasool, Saima Iftikhar, Anam Amir, Waqar Hussain
Pyrazinamide is known to be the most effective treatment against tuberculosis disease and is known to have bacteriostatic action. By targeting the bacterial spores, this drug reduces the chances for the progression of the infection in organisms. In recent years, increased instances of the drug resistance of bacterial strains are reported. Pyrazinamidase, activator for pyrazinamide, leads to resistance against the drug due to mutagenicity across the world. The present study aimed at the quantum mechanistic analysis of mutations in pyrazinamidase to gain insights into the mechanism of this enzyme...
December 24, 2017: Journal of Molecular Graphics & Modelling
Yogesh Narkhede, Benjamin Merget, Steffen Wagner, Christoph Sotriffer
Developing reliable structure-based activity prediction models for a particular ligand series can be challenging if the target is flexible and the affinity range of the training compounds is narrow. For a data set of 44 pyrrolidine carboxamide inhibitors of the mycobacterial enoyl-ACP-reductase InhA this proved to be case, as scoring methods of various origin and complexity did not succeed in providing practically useful correlations with experimental inhibition data. In contrast, logistic regression models for activity-based classification trained with combinations of scoring functions led to good separation of the more active inhibitors from the weakest compounds...
December 24, 2017: Journal of Molecular Graphics & Modelling
Jitendra Maharana
Inflammasomes are the multi-protein caspase-activating complexes mainly assembled by the sensor proteins (NLRs/ALRs), adaptor molecule (ASC) and effector molecule pro-caspase-1 for the production and release of proinflammatory cytokines, IL-1β and IL-18. NLRP1 is the first NLR known to assemble the multi-protein complex. Unlike NLRP3, NLRP1 has an additional effector binding domain (CARD) at the carboxyl-terminal, which is reported to interact with pro-caspase-1 (precluding the recruitment of ASC) for the transmission of danger signals...
December 24, 2017: Journal of Molecular Graphics & Modelling
Davood Farmanzadeh, Mahsa Ghaderi
In this study, the interaction of zero generation (G0) of polyamidoamine (PAMAM) dendrimer with trans isomer of Picoplatin anticancer drug (AMD) has been investigated by density functional theory. According to the structure of dendrimer and drug, two types of dendrimer cavities that can interact with the drugs can be formed in drug-loaded PAMAM dendrimer in which AMD drug can be located inside the PAMAM cavities through Cl and NH3 heads. The results have indicated that the interaction of PAMAM dendrimer with picoplatin anticancer drugs is physisorption...
December 20, 2017: Journal of Molecular Graphics & Modelling
Pallavi Mohanty, Sonika Bhatnagar
Focal adhesion kinase (FAK) is required for signaling in the heart. S910 phosphorylated FAK is known to cause pathological cardiac hypertrophy. The switching of FAK between its inactive (-i), activated (-a) and hyperactive (-h) state is controlled by phosphorylation. FAK consists of three domains, namely: FERM, Kinase, and FAT joined by linkers L1 and L2. The structural basis of FAK phosphorylation and signaling to the downstream pathways is not understood. In this work, we carried out homology modeling and domain assembly of full length human iFAK and aFAK...
December 19, 2017: Journal of Molecular Graphics & Modelling
Sumith Yd, Shalabh C Maroo
Two-dimensional (2D) pressure field estimation in molecular dynamics (MD) simulations has been done using three-dimensional (3D) pressure field calculations followed by averaging, which is computationally expensive due to 3D convolutions. In this work, we develop a direct 2D pressure field estimation method which is much faster than 3D methods without losing accuracy. The method is validated with MD simulations on two systems: a liquid film and a cylindrical drop of argon suspended in surrounding vapor.
December 15, 2017: Journal of Molecular Graphics & Modelling
Taro Uchida, Masaki Wakasugi, Takahiro Kitamura, Tomomi Yamamoto, Mitsutoshi Asakura, Ryoichi Fujiwara, Tomoo Itoh, Hideaki Fujii, Shuichi Hirono
Dipeptidyl peptidase-IV (DPP-IV), an enzyme that degrades incretins-hormones that promote insulin secretion-is a therapeutic target for type 2 diabetes, with a number of its inhibitors having been launched as therapies for diabetes. Since adverse effects of these inhibitors have recently been reported, the development of novel DPP-IV inhibitors with higher efficacy and safety is required. We, therefore, screened for novel DPP-IV inhibitors using the combination of an in silico drug discovery technique and a DPP-IV assay system...
December 14, 2017: Journal of Molecular Graphics & Modelling
Saeid Onsori, Elham Alipour
We explored the reactivity, and electronic sensitivity of the synthesized B12N12 nanocluster to cisplatin (CP) anticancer drug by means of density functional theory calculations. It is predicted that the drug prefers to be adsorbed simultaneously from its hydrogen and halogen atoms on a BN bond of the BN nanocluster with adsorption energy about -14.9 kcal/mol. The electronic properties of B12N12 nanocluster are predicted to be sensitive to the CP drug and it benefits from a short recovery time about 81 ms at room temperature...
December 11, 2017: Journal of Molecular Graphics & Modelling
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