Molecular dynamics investigation of the active site dynamics of mycobacterial cyclopropane synthase during various stages of the cyclopropanation process

Fragment tailoring strategy to design novel chemical entities as potential binders of novel corona virus main protease

The recent pandemic of severe acute respiratory syndrome-coronavirus2 (SARS-CoV-2) infection (COVID-19) has put the world on serious alert. The main protease of SARS-CoV-2 (SARS-CoV-2-MPro) cleaves the long polyprotein chains to release functional proteins required for replication of the virus and thus is a potential drug target to design new chemical entities in order to inhibit the viral replication in human cells. The current study employs state of art computational methods to design novel molecules by linking molecular fragments which specifically bind to different constituent sub-pockets of the SARS-CoV-2-MPro binding site. A huge library of 191678 fragments was screened against the binding cavity of SARS-CoV-2-MPro and high affinity fragments binding to adjacent sub-pockets were tailored to generate new molecules. These newly formed molecules were further subjected to molecular docking, ADMET filters and MM-GBSA binding energy calculations to select 17 best molecules (named as MP-In1 to MP-In17), which showed comparable binding affinities and interactions with the key binding site residues as the reference ligand. The complexes of these 17 molecules and the reference molecule with SARS-CoV-2-MPro, were subjected to molecular dynamics simulations, which assessed the stabilities of their binding with SARS-CoV-2-MPro. Fifteen molecules were found to form stable complexes with SARS-CoV-2-MPro. These novel chemical entities designed specifically according to the pharmacophoric requirements of SARS-CoV-2-MPro binding pockets showed good synthetic feasibility and returned no exact match when searched against chemical databases. Considering their interactions, binding efficiencies and novel chemotypes, they can be further evaluated as potential starting points for SARS-CoV-2 drug discovery.

Hybrid Dynamic Pharmacophore Models as Effective Tools to Identify Novel Chemotypes for Anti-TB Inhibitor Design: A Case Study With Mtb-DapB

Antimicrobial resistance (AMR) is one of the most serious global public health threats as it compromises the successful treatment of deadly infectious diseases like tuberculosis. New therapeutics are constantly needed but it takes a long time and is expensive to explore new biochemical space. One way to address this issue is to repurpose the validated targets and identify novel chemotypes that can simultaneously bind to multiple binding pockets of these targets as a new lead generation strategy. This study reports such a strategy, dynamic hybrid pharmacophore model (DHPM), which represents the combined interaction features of different binding pockets contrary to the conventional approaches, where pharmacophore models are generated from single binding sites. We have considered Mtb-DapB, a validated mycobacterial drug target, as our model system to explore the effectiveness of DHPMs to screen novel unexplored compounds. Mtb-DapB has a cofactor binding site (CBS) and an adjacent substrate binding site (SBS). Four different model systems of Mtb-DapB were designed where, either NADPH/NADH occupies CBS in presence/absence of an inhibitor 2, 6-PDC in the adjacent SBS. Two more model systems were designed, where 2, 6-PDC was linked to NADPH and NADH to form hybrid molecules. The six model systems were subjected to 200 ns molecular dynamics simulations and trajectories were analyzed to identify stable ligand-receptor interaction features. Based on these interactions, conventional pharmacophore models (CPM) were generated from the individual binding sites while DHPMs were created from hybrid-molecules occupying both binding sites. A huge library of 1,563,764 publicly available molecules were screened by CPMs and DHPMs. The screened hits obtained from both types of models were compared based on their Hashed binary molecular fingerprints and 4-point pharmacophore fingerprints using Tanimoto, Cosine, Dice and Tversky similarity matrices. Molecules screened by DHPM exhibited significant structural diversity, better binding strength and drug like properties as compared to the compounds screened by CPMs indicating the efficiency of DHPM to explore new chemical space for anti-TB drug discovery. The idea of DHPM can be applied for a wide range of mycobacterial or other pathogen targets to venture into unexplored chemical space.

Free enzyme dynamics of CmaA3 and CmaA2 cyclopropane mycolic acid synthases from Mycobacterium tuberculosis: Insights into residues with potential significance in cyclopropanation

Mycolic acids are long chain alpha-alkyl beta-hydroxy fatty acids that are major constituents of the cell wall of Mycobacterium tuberculosis. M. tuberculosis produces three main types of mycolic acids, alpha mycolic acids and keto and methoxy mycolic acids. Cycloproponated mycolic acids make the cell wall less permeable, contribute to antibiotic resistance and host immunomodulation and protect from injury. Cyclopropanation is catalyzed by enzymes of the Cyclopropane Mycolic Acid Synthase (CMAS) family. In the current study, we addressed two CMAS enzymes, proximal alpha cyclopropane mycolic acid synthase (PcaA/CmaA3) and keto cyclopropane Mycolic acid synthase (CmaA2). All-atom Molecular Dynamics (MD) simulations were performed for these enzymes for a timeframe of 100ns each (in triplicate), using GROMACS. Based on the PDB structures of apo and holo states of related CMAS enzymes, we generated a framework which helped us correlate active or inactive states of the enzymes to different conformations sampled by the enzymes during MD simulations. Dynamics suggested that the free or unbound enzymes have intrinsic memory and sample different states of catalysis even in the absence of the substrate/cofactor. Additionally, we find that F200, P201 and W204 may have functional significance. MD simulation of CmaA2 was performed with the objective of gaining insights into the putative role of a loop insert. Analysis showed that acidic residues of this loop possibly play an important role during the active state by forming salt bridges. The insights gained in this study can potentially be utilized for design of effective inhibitors against CMAS enzymes.

Structural Basis for the Influence of A1, 5A, and W51W57 Mutations on the Conductivity of the Geobacter sulfurreducens Pili

The metallic-like conductivity of the Geobacter sulfurreducens pilus and higher conductivity of its mutants reflected that biological synthesis can be utilized to improve the properties of electrically conductive pili. However, the structural basis for diverse conductivities of nanowires remains uncertain. Here, the impacts of point mutations on the flexibility and stability of pilins were investigated based on molecular dynamics simulations. Structures of the G. sulfurreducens pilus and its mutants were constructed by Rosetta. Details of the structure (i.e., electrostatic properties, helical parameters, residue interaction network, distances between amino acids, and salt bridges) were analyzed by PDB2PQR, Rosetta, RING, PyMOL, and VMD, respectively. Changes in stability, flexibility, residue interaction, and electrostatic properties of subunits directly caused wild-type pilin and its mutants assemble different structures of G. sulfurreducens pili. By comparing the structures of pili with different conductivities, the mechanism by which the G. sulfurreducens pilus transfers electron along pili was attributed, at least in part, to the density of aromatic rings, the distances between neighboring aromatic rings, and the local electrostatic environment around aromatic contacts. These results provide new insight into the potential for the biological synthesis of highly electrically conductive, nontoxic nanowires.

Dynamics based pharmacophore models for screening potential inhibitors of mycobacterial cyclopropane synthase

The therapeutic challenges in the treatment of tuberculosis demand multidisciplinary approaches for the identification of potential drug targets as well as fast and accurate techniques to screen huge chemical libraries. Mycobacterial cyclopropane synthase (CmaA1) has been shown to be essential for the survival of the bacteria due to its critical role in the synthesis of mycolic acids. The present study proposes pharmacophore models based on the structure of CmaA1 taking into account its various states in the cyclopropanation process, and their dynamic nature as assessed using molecular dynamics (MD) simulations. The qualities of these pharmacophore models were validated by mapping 23 molecules that have been previously reported to exhibit inhibitory activities on CmaA1. Additionally, 1398 compounds that have been shown to be inactive for tuberculosis were collected from the ChEMBL database and were screened against the models for validation. The models were further validated by comparing the results from pharmacophore mapping with the results obtained from docking these molecules with the respective protein structures. The best models are suggested by validating all the models based on their screening abilities and by comparing with docking results. The models generated from the MD trajectories were found to perform better than the one generated based on the crystal structure demonstrating the importance of incorporating receptor flexibility in drug design.