Introduction: The molecular mechanics energies combined with the Poisson–Boltzmann or generalized Born and surface area continuum solvation (MM/PBSA and MM/GBSA) methods are popular approaches to estimate the free energy of the binding of small ligands to biological macromolecules. They are typically based on molecular dynamics simulations of the receptor–ligand complex and are therefore intermediate in both accuracy and computational effort between empirical scoring and strict alchemical perturbation methods. They have been applied to a large number of systems with varying success.Areas covered: The authors review the use of MM/PBSA and MM/GBSA methods to calculate ligand-binding affinities, with an emphasis on calibration, testing and validation, as well as attempts to improve the methods, rather than on specific applications.Expert opinion: MM/PBSA and MM/GBSA are attractive approaches owing to their modular nature and that they do not require calculations on a training set. They have been used success...

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The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities

Statistical Methods For Agricultural Workers

Molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) and molecular mechanics generalized Born surface area (MM/GBSA) are arguably very popular methods for binding free energy prediction since they are more accurate than most scoring functions of molecular docking and less computationally demanding than alchemical free energy methods. MM/PBSA and MM/GBSA have been widely used in biomolecular studies such as protein folding, protein-ligand binding, protein-protein interaction, etc. In this review, methods to adjust the polar solvation energy and to improve the performance of MM/PBSA and MM/GBSA calculations are reviewed and discussed. The latest applications of MM/GBSA and MM/PBSA in drug design are also presented. This review intends to provide readers with guidance for practically applying MM/PBSA and MM/GBSA in drug design and related research fields.

End-Point Binding Free Energy Calculation with MM/PBSA and MM/GBSA: Strategies and Applications in Drug Design

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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Recent Developments and Applications of the MMPBSA Method.

Molecular mechanics/Poisson-Boltzmann (Generalized-Born) surface area is one of the most popular methods to estimate binding free energies. This method has been proven to balance accuracy and computational efficiency, especially when dealing with large systems. As a result of its popularity, several programs have been developed for performing MM/PB(GB)SA calculations within the GROMACS community. These programs, however, present several limitations. Here we present gmx_MMPBSA, a new tool to perform end-state free energy calculations from GROMACS molecular dynamics trajectories. gmx_MMPBSA provides the user with several options, including binding free energy calculations with different solvation models (PB, GB, or 3D-RISM), stability calculations, computational alanine scanning, entropy corrections, and binding free energy decomposition. Noteworthy, several promising methodologies to calculate relative binding free energies such as alanine scanning with variable dielectric constant and interaction entropy have also been implemented in gmx_MMPBSA. Two additional tools-gmx_MMPBSA_test and gmx_MMPBSA_ana-have been integrated within gmx_MMPBSA to improve its usability. Multiple illustrating examples can be accessed through gmx_MMPBSA_test, while gmx_MMPBSA_ana provides fast, easy, and efficient access to different graphics plotted from gmx_MMPBSA output files. The latest version (v1.4.3, 26/05/2021) is available free of charge (documentation, test files, and tutorials included) at https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA.

gmx_MMPBSA: A New Tool to Perform End-State Free Energy Calculations with GROMACS.

Molecular mechanics Poisson–Boltzmann surface area (MM-PBSA), a method to estimate interaction free energies, has been increasingly used in the study of biomolecular interactions. Recently, this method has also been applied as a scoring function in computational drug design. Here a new tool g_mmpbsa, which implements the MM-PBSA approach using subroutines written in-house or sourced from the GROMACS and APBS packages is described. g_mmpbsa was developed as part of the Open Source Drug Discovery (OSDD) consortium. Its aim is to integrate high-throughput molecular dynamics (MD) simulations with binding energy calculations. The tool provides options to select alternative atomic radii and different nonpolar solvation models including models based on the solvent accessible surface area (SASA), solvent accessible volume (SAV), and a model which contains both repulsive (SASA-SAV) and attractive components (described using a Weeks–Chandler–Andersen like integral method). We showcase the effectiveness of the tool ...

g_mmpbsa--a GROMACS tool for high-throughput MM-PBSA calculations.

We sought to clarify on the hitherto unresolved role of N-terminal transmembrane segments (TMS) of cytochrome P450 (CYP) and its’ reductase (CPR) in protein interaction/catalysis. TMS analyses show little evolutionary conservation in CYPs. The conserved CPR’s TMS poses limited scope for predictable/consistent hetero-recognition with the wide bevy of CYPs’ TMS, as evident from preliminary analyses and TMhit server predictions for inter-helical binding. Further, experimentations with four different CPR preparations (preps) and two liver microsomal CYPs (2C9 and 2E1) shows that the hydroxylated product formation rate is not quantitatively correlated to the extent of integrity of the CPR N-terms. Incorporation of cytochrome b5 in some reactions afforded similar rates while employing either fully intact or partially intact CPR. A survey of literature shows that liver microsomal CYPs function quite well even without the TMS or with significantly altered TMS. These observations negate the hypothesis that N-term TMS of CPR or CYP is obligatory for CYP–CPR interaction and catalysis. Also, in CYP2E1-mediated hydroxylation of para-nitrophenol, the extent of intactness or truncation did not significantly affect the CPR preps’ catalytic role at very low or high substrate concentrations. To interpret these results, we draw support from recently published research on reduced nicotinamide adenide dinucleotide phosphate oxidase (Takac et al., J Biol Chem, 286:13304–13313, 2011) and from our pertinent earlier works. We infer that CPR’ free TMS segment could alter the diffusible reactive oxygen species’ dynamics in the microenvironment, thereby altering the reaction outcome. Based on the evidence, we conclude that TMS merely facilitates “interaction/catalysis” by anchoring the CYP and CPR in the lipid interface.

What is the Functional Role of N-terminal Transmembrane Helices in the Metabolism Mediated by Liver Microsomal Cytochrome P450 and its Reductase?

The 12-subunit RNA polymerase II enzyme in yeasts and higher eukaryotic cells is important for transcription of protein-coding genes. Its fourth and seventh largest subunits named Rpb4 and Rpb7, respectively, display some unique features that distinguish them from the remaining subunits of this enzyme. These two subunits also bind to each other forming a complex in archaebacteria, yeasts, plants and humans. Our knowledge about the structure and functions of this complex has greatly advanced in recent years. These subunits were initially considered to be important only for initiation of transcription and stress response. However, recent evidence suggests that they are not only involved in transcription, but also in DNA repair, mRNA export and decay as well as translation, highlighting the roles of this heterodimer in diverse biological processes. In this article, we review the current status of these two subunits and discuss attributes of their structure and function across organisms.

Rpb4 and Rpb7: multifunctional subunits of RNA polymerase II

Edible oil seed crops, such as rapeseed, sunflower, soyabean and safflower and non-edible seed oil plantation crops Jatropha and Pongamia have proved to be internationally viable commercial sources of vegetable oils for biodiesel production. Considering the paucity of edible oils and unsustainability of arable land under perennial plantation of Jatropha and Pongamia in countries such as India, the prospects of seed oil producing Cleome viscosa, an annual wild short duration plant species of the Indogangetic plains, were evaluated for it to serve as a resource for biodiesel. The seeds of C. viscosa resourced from its natural populations growing in Rajasthan, Haryana and Delhi areas of Aravali range were solvent extracted to obtain the seed oil. The oil was observed to be similar in fatty acid composition to the non-edible oils of rubber, Jatropha and Pongamia plantation crops and soybean, sunflower, safflower, linseed and rapeseed edible oil plants in richness of unsaturated fatty acids. The Cleome oil shared the properties of viscosity, density, saponification and calorific values with the Jatropha and Pongamia oils, except that it was comparatively acidic. The C. viscosa biodiesel had the properties of standard biodiesel specified by ASTM and Indian Standard Bureau, except that it had low oxidation stability. It proved to be similar to Jatropha biodiesel except in cloud point, pour point, cold filter plugging point and oxidation stability. In view of the annual habit of species and biodiesel quality, it can be concluded that C. viscosa has prospects to be developed into a short-duration biodiesel crop.

http://nopr.niscair.res.in/bitstream/123456789/14333/1/IJEB%2050%287%29%20502-510.pdf

Biodiesel production from seed oil of Cleome viscosa L.

In an earlier study at our laboratory showed that the biodiesel derived from the seed oil of the annual herbaceous medicinal weed plant Cleome viscosa Linn. possesses properties similar to the commercial biodiesel produced from Jatropha seed oil. Here, the possibilities of domestication of C. viscosa were examined. With this objective, 15 accessions from Aravali range in North-West India and two from North-East India were evaluated for phenotypic and genetic variability. The accessions were cultivated in four seasons from May to November 2009 at New Delhi by growing them in randomized block design replicated four times. The accessions were studied for 6 qualitative and 13 agronomic characters and significant genetic variability in all the agronomic traits was observed. On the basis of morphological features, the accessions fell into two groups: a small leaved group and a large leaved group. While the small leaved group comprised of accessions from Rajasthan, the large leaved group included accessions from different locations in North-west and NorthEast India. One of the small leaved accessions called CVR14 was identified as a putative high yielding accession. The JulyOctober (or monsoon-autumn) season of about 13-15 weeks was observed to be the most suitable period for obtaining rainfed crop of C. viscosa CVR14. The DNA fingerprinting based analysis of hierarchical relationships between accessions demonstrated that large leaved and small leaved accessions were inter-related. The results indicated that C. viscosa accessions from diverse locations perhaps comprised a single complex.

http://nopr.niscair.res.in/bitstream/123456789/14408/1/IJNPR%203%282%29%20246-255.pdf

Rashmi Kumari

Papers

g_mmpbsa--a GROMACS tool for high-throughput MM-PBSA calculations.

What is the Functional Role of N-terminal Transmembrane Helices in the Metabolism Mediated by Liver Microsomal Cytochrome P450 and its Reductase?

Rpb4 and Rpb7: multifunctional subunits of RNA polymerase II

Biodiesel production from seed oil of Cleome viscosa L.

Variability in the accessions from Aravali range assessed for domestication of the Cleomaceae biodiesel plant Cleome viscosa Linn.