Insight into free energy and dynamic cross-correlations of residue for binding affinity of antibody and receptor binding domain SARS-CoV-2.

SARS-CoV-2 virus continues to evolve and mutate causing most of the mutated variants resist to many of the therapeutic monoclonal antibodies (mAbs). Despite several mAbs retained neutralizing capability for Omicron BA.1 and BA.2, reduction in neutralization potency was reported. Hence, effort of searching for mAb that is broader in neutralization breadth without losing the neutralizing ability is continued. MW06 was reported with capability in neutralizing most of the variants of concern (VOC) and it binds to the conserved region (left flank) near epitope mAb sotrovimab (S309). In this study, binding affinity of mAb MW06 and its cocktail formulation with MW05 for receptor binding domain (RBD) SARS-CoV-2 virus was investigated under molecular dynamics simulations (MDs). Binding free energies computed by Molecular Mechanics Generalised Born Surface Area (MM-GBSA) algorithm predicted the binding affinity of MW06 for RBD BA.1 (-53 kcal/mol) as strong as RBD wildtype (-58 kcal/mol) while deterioration was observed for RBD BA.2 (-43 kcal/mol). Alike S309 and MW06, simulated cocktail mAb (MW05 and MW06)-RBD interactions suggested the neutralizing capability of the cocktail formulation for RBD BA.1 and BA.2 reduced. Meanwhile, residue pairs that favour the communication between the mAb and RBD have been identified by decomposing the free energy per pairwise residue basis. Apart from understanding the effects of mutation occurred in the RBD region on human angiotensin-converting enzyme 2 (hACE2) binding, impact of heavily mutated RBD on mAb-RBD interactions was investigated in this study as well. In addition to energetic profile obtained from MDs, plotting the dynamics cross-correlation map of the mAb-RBD complex under elastic network model (ENM) was aimed to understand the cross-correlations between residue fluctuations. It allows simple and rapid analysis on the motions or dynamics of the protein residues of mAbs and RBD in complex. Protein residues having correlated motions are normally part of the structural domains of the protein and their respective motions and protein function are related. Motion of mutated RBD residues and mAb residues was less correlated while their respective interactions energy computed to be higher. The combined techniques of MDs and ENM offered simplicity in understanding dynamics and energy contribution that explain binding affinity of mAb-RBD complexes.

Magnetic carbon nanofiber composite adsorbent through green in-situ conversion of bacterial cellulose for highly efficient removal of bisphenol A.

A magnetic carbon nanofiber sorbent was facilely synthesized from bio-based bacterial cellulose and FeCl3via impregnation, freeze-drying, followed by pyrolysis at 700 °C, without additional activation or nanofiber fabrication. The obtained material possessed intrinsic 3D naturally fibrous and porous structure with good magnetization. The adsorption results showed that the adsorption capacity of the prepared adsorbent towards bisphenol A (BPA) was as high as 618 mg/g, outperforming other adsorbents. Moreover, recycling the adsorbent for 10 consecutive cycles retained 96% of initial adsorption efficiency. The magnetic sorbent can maintain good magnetic properties even with recycling. Hence, the use of bacterial cellulose as a renewable carbon nanofiber precursor and FeCl3 as a source of magnetic particles, and a green pore generating agent in the present protocol, lead to a superior magnetic carbon nanofiber adsorbent with sustainable characteristics.

A facile one-pot green synthesis of gold nanoparticle-graphene-PEDOT:PSS nanocomposite for selective electrochemical detection of dopamine.

A facile one-pot and green method was developed to prepare a nanocomposite of gold nanoparticle (AuNP), graphene (GP) and poly(3,4-ethylenedioxythiophene) polystyrene sulfonate (PEDOT:PSS). Graphene was first electro-exfoliated in a polystyrene sulfonate solution, followed by a one-step simultaneous in situ formation of gold nanoparticle and PEDOT. The as-synthesized aqueous dispersion of AuNP-GP-PEDOT:PSS was thereafter used to modify the glassy carbon electrode (GCE). For the first time, the quaternary composite between AuNP, GP, PEDOT and PSS was used for selective determination of dopamine (DA) and uric acid (UA) in the presence of ascorbic acid (AA). In comparison to a bare GCE, the nanocomposite electrode shows considerably higher electrocatalytic activities toward the oxidation of DA and UA due to a synergistic effect between AuNP, GP, PEDOT and PSS. Using differential pulse voltammetry (DPV), selective determination of DA and UA in the presence of AA could be achieved with a peak potential separation of 110 mV between DA and UA. The sensor exhibits wide linear responses for DA and UA in the ranges of 1 nM to 300 µM and 10 µM to 1 mM with detection limits (S/N = 3) of 100 pM and 10 µM, respectively. Furthermore, the proposed sensor was also successfully used to determine DA in a real pharmaceutical injection sample as well as DA and UA in human serum with satisfactory recovery results.

Elucidating the structural basis of diphenyl ether derivatives as highly potent enoyl-ACP reductase inhibitors through molecular dynamics simulations and 3D-QSAR study.

Diphenyl ether derivatives are good candidates for anti-tuberculosis agents that display a promising potency for inhibition of InhA, an essential enoyl-acyl carrier protein (ACP) reductase involved in fatty acid biosynthesis pathways in Mycobacterium tuberculosis. In this work, key structural features for the inhibition were identified by 3D-QSAR CoMSIA models, constructed based on available experimental binding properties of diphenyl ether inhibitors, and a set of four representative compounds was subjected to MD simulations of inhibitor-InhA complexes for the calculation of binding free energies. The results show that bulky groups are required for the R1 substituent on the phenyl A ring of the inhibitors to favor a hydrophobic pocket formed by residues Phe149, Met155, Pro156, Ala157, Tyr158, Pro193, Met199, Val203, Leu207, Ile215, and Leu218. Small substituents with a hydrophilic property are required at the R3 and R4 positions of the inhibitor phenyl B rings to form hydrogen bonds with the backbones of Gly96 and Met98, respectively. For the R2 substituent, small substituents with simultaneous hydrophilic or hydrophobic properties are required to favor the interaction with the pyrophosphate moiety of NAD(+) and the methyl side chain of Ala198, respectively. The reported data provide structural guidance for the design of new and potent diphenyl ether-based inhibitors with high inhibitory activities against M. tuberculosis InhA.

Substrate induced structural and dynamics changes in human phosphomevalonate kinase and implications for mechanism.

Phosphomevalonate kinase (PMK) catalyzes an essential step in the mevalonate pathway, which is the only pathway for synthesis of isoprenoids and steroids in humans. PMK catalyzes transfer of the gamma-phosphate of ATP to mevalonate 5-phosphate (M5P) to form mevalonate 5-diphosphate. Bringing these phosphate groups in proximity to react is especially challenging, given the high negative charge density on the four phosphate groups in the active site. As such, conformational and dynamics changes needed to form the Michaelis complex are of mechanistic interest. Herein, we report the characterization of substrate induced changes (Mg-ADP, M5P, and the ternary complex) in PMK using NMR-based dynamics and chemical shift perturbation measurements. Mg-ADP and M5P K(d)'s were 6-60 microM in all complexes, consistent with there being little binding synergy. Binding of M5P causes the PMK structure to compress (tau(c) = 13.5 nsec), whereas subsequent binding of Mg-ADP opens the structure up (tau(c) = 15.6 nsec). The overall complex seems to stay very rigid on the psec-nsec timescale with an average NMR order parameter of S(2) approximately 0.88. Data are consistent with addition of M5P causing movement around a hinge region to permit domain closure, which would bring the M5P domain close to ATP to permit catalysis. Dynamics data identify potential hinge residues as H55 and R93, based on their low order parameters and their location in extended regions that connect the M5P and ATP domains in the PMK homology model. Likewise, D163 may be a hinge residue for the lid region that is homologous to the adenylate kinase lid, covering the "Walker-A" catalytic loop. Binding of ATP or ADP appears to cause similar conformational changes; however, these observations do not indicate an obvious role for gamma-phosphate binding interactions. Indeed, the role of gamma-phosphate interactions may be more subtle than suggested by ATP/ADP comparisons, because the conservative O to NH substitution in the beta-gamma bridge of ATP causes a dramatic decrease in affinity and induces few chemical shift perturbations. In terms of positioning of catalytic residues, binding of M5P induces a rigidification of Gly21 (adjacent to the catalytically important Lys22), although exchange broadening in the ternary complex suggests some motion on a slower timescale does still occur. Finally, the first nine residues of the N-terminus are highly disordered, suggesting that they may be part of a cleavable signal or regulatory peptide sequence.

Chaetoglobins A and B, two unusual alkaloids from endophytic Chaetomium globosum culture.

Chaetoglobins A (1) and B (2), two azaphilone alkaloid dimers with an unprecedented skeleton, were characterized from an endophytic fungus Chaetomium globosum with the former ascertained to be a significant cytotoxin valuable for anti-tumor drug discovery.

Novel 2-chloro-8-arylthiomethyldipyridodiazepinone derivatives with activity against HIV-1 reverse transcriptase.

Based on the molecular modeling analysis against Y181C HIV-1 RT, dipyridodiazepinone derivatives containing an unsubstituted lactam nitrogen and 2-chloro-8-arylthiomethyl were synthesized via an efficient route. Some of them were evaluated for their antiviral activity against HIV-1 RT subtype E and were found to exhibit virustatic activity comparable to some clinically used therapeutic agents.