Improved GAFF2 parameters for fluorinated alkanes and mixed hydro- and fluorocarbons

Träg, Johannes; Zahn, Dirk

doi:10.1007/s00894-018-3911-5

Cited by 42 publications

(23 citation statements)

References 13 publications

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“…Amber Tools 19 [ 59 ] was used to create the topology and coordinate files of each system. The second-generation General AMBER Force Field (GAFF2) [ 60 ] with AM1-BCC partial charges as implemented in Antechamber [ 61 ] was used for the host and guest, TIP3P [ 62 ] was used for water, and the Joung and Cheatham parameters were used for the one chloride ion [ 63 ], which was added to neutralize the +1 charge of the guest. The entropic contribution of this chloride is not considered here, assuming the ion to be weakly interacting with the host and guest and therefore constant and canceling in the difference.…”

Section: Methodsmentioning

confidence: 99%

Energy–entropy method using multiscale cell correlation to calculate binding free energies in the SAMPL8 host–guest challenge

Ali

Chakravorty

Kalayan

et al. 2021

J Comput Aided Mol Des

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Free energy drives a wide range of molecular processes such as solvation, binding, chemical reactions and conformational change. Given the central importance of binding, a wide range of methods exist to calculate it, whether based on scoring functions, machine-learning, classical or electronic structure methods, alchemy, or explicit evaluation of energy and entropy. Here we present a new energy–entropy (EE) method to calculate the host–guest binding free energy directly from molecular dynamics (MD) simulation. Entropy is evaluated using Multiscale Cell Correlation (MCC) which uses force and torque covariance and contacts at two different length scales. The method is tested on a series of seven host–guest complexes in the SAMPL8 (Statistical Assessment of the Modeling of Proteins and Ligands) “Drugs of Abuse” Blind Challenge. The EE-MCC binding free energies are found to agree with experiment with an average error of 0.9 kcal mol−1. MCC makes clear the origin of the entropy changes, showing that the large loss of positional, orientational, and to a lesser extent conformational entropy of each binding guest is compensated for by a gain in orientational entropy of water released to bulk, combined with smaller decreases in vibrational entropy of the host, guest and contacting water.

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Section: Methodsmentioning

confidence: 99%

Energy–entropy method using multiscale cell correlation to calculate binding free energies in the SAMPL8 host–guest challenge

Ali

Chakravorty

Kalayan

et al. 2021

J Comput Aided Mol Des

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“…The physiological pH was retained by maintaining the ionic strength of 0.15 M. The protein forcefield, ff14SB [48] was applied to generate the protein topology. The GAFF2 [49] force field was used to generate the ligand topology. The PMEMD.CUDA module [50] was considered to perform the simulation.…”

Section: Molecular Dynamics Simulationmentioning

confidence: 99%

Pharmacoinformatics-based identification of transmembrane protease serine-2 inhibitors from Morus Alba as SARS-CoV-2 cell entry inhibitors

et al. 2021

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Transmembrane protease serine-2 (TMPRSS2) is a cell-surface protein expressed by epithelial cells of specific tissues including those in the aerodigestive tract. It helps the entry of novel coronavirus (n-CoV) or Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in the host cell. Successful inhibition of the TMPRSS2 can be one of the crucial strategies to stop the SARS-CoV-2 infection. In the present study, a set of bioactive molecules from Morus alba Linn. were screened against the TMPRSS2 through two widely used molecular docking engines such as Autodock vina and Glide. Molecules having a higher binding affinity toward the TMPRSS2 compared to Camostat and Ambroxol were considered for in-silico pharmacokinetic analyses. Based on acceptable pharmacokinetic parameters and drug-likeness, finally, five molecules were found to be important for the TMPRSS2 inhibition. A number of bonding interactions in terms of hydrogen bond and hydrophobic interactions were observed between the proposed molecules and ligand-interacting amino acids of the TMPRSS2. The dynamic behavior and stability of best-docked complex between TRMPRSS2 and proposed molecules were assessed through molecular dynamics (MD) simulation. Several parameters from MD simulation have suggested the stability between the protein and ligands. Binding free energy of each molecule calculated through MM-GBSA approach from the MD simulation trajectory suggested strong affection toward the TMPRSS2. Hence, proposed molecules might be crucial chemical components for the TMPRSS2 inhibition. Graphic abstract

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“…Molecular dynamics simulations were carried out on Amber18 package 22 . Ligand parameters were obtained from general Amber force field (GAFF2) 23 and AM1 BCC method was used to derive the charges. Bonded and non-bonded parameters for protein were obtained from Amber 14SB force field.…”

Section: Molecular Dynamics Simulationsmentioning

confidence: 99%

In-Silico Drug Repurposing for Targeting SARS-CoV-2 Mpro

Sharma¹,

Deep

2020

Preprint

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COVID-19, caused by novel coronavirus or SARS-CoV-2, is a viral disease which has infected millions worldwide. Considering the urgent need of the drug for fighting against this infectious disease, we performed in-silico drug repurposing. The main protease (Mpro) is one of the best characterized drug targets among coronaviruses, therefore, this was screened for already known drugs, including chemical constituents of Ayurvedic drugs, using docking and MD simulation. The results suggest EGCG, withaferin A and artesunate may act as potential inhibitors of the main protease (Mpro).

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Improved GAFF2 parameters for fluorinated alkanes and mixed hydro- and fluorocarbons

Cited by 42 publications

References 13 publications

Energy–entropy method using multiscale cell correlation to calculate binding free energies in the SAMPL8 host–guest challenge

Energy–entropy method using multiscale cell correlation to calculate binding free energies in the SAMPL8 host–guest challenge

Pharmacoinformatics-based identification of transmembrane protease serine-2 inhibitors from Morus Alba as SARS-CoV-2 cell entry inhibitors

In-Silico Drug Repurposing for Targeting SARS-CoV-2 Mpro

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