Jitti Niramitranon’s research while affiliated with Kasetsart University and other places

Diabetes mellitus is a chronic metabolic disease involving continued elevated blood glucose levels. It is a leading cause of mortality and reduced life expectancy. Glycated human serum albumin (GHSA) has been reported to be a potential diabetes biomarker. A nanomaterial-based aptasensor is one of the effective techniques to detect GHSA. Graphene quantum dots (GQDs) have been widely used in aptasensors as an aptamer fluorescence quencher due to their high biocompatibility and sensitivity. GHSA-selective fluorescent aptamers are first quenched upon binding to GQDs. The presence of albumin targets results in the release of aptamers to albumin and consequently fluorescence recovery. To date, the molecular details on how GQDs interact with GHSA-selective aptamers and albumin remain limited, especially the interactions of an aptamer-bound GQD (GQDA) with an albumin. Thus, in this work, molecular dynamics simulations were used to reveal the binding mechanism of human serum albumin (HSA) and GHSA to GQDA. The results show the rapid and spontaneous assembly of albumin and GQDA. Multiple sites of albumins can accommodate both aptamers and GQDs. This suggests that the saturation of aptamers on GQDs is required for accurate albumin detection. Guanine and thymine are keys for albumin-aptamer clustering. GHSA gets denatured more than HSA. The presence of bound GQDA on GHSA widens the entrance of drug site I, resulting in the release of open-chain glucose. The insight obtained here will serve as a base for accurate GQD-based aptasensor design and development.

Porcine serum albumin (PSA) is one of the promising biomarkers for pork detection. Pork contamination is a serious concern for the global halal food industry since many manufacturers mix pork into halal beef products to reduce production costs. Many studies have thus been devoted to designing effective PSA-detecting biosensors. PSA is closely related to Bovine serum albumin (BSA); therefore; the molecular insight into PSA characteristics becomes crucial to identify PSA. To understand PSA properties, Molecular dynamic (MD) simulations were employed. The three-dimensional structures of PSA were obtained from homology modelling and Alphafold. Both models give similar results. PSA seems to have high hydrophobicity and unique electrostatic properties. Unlike BSA, PSA has no large electropositive patch on the rear of domain III. This property can be used to differentiate PSA from BSA. In the case of drug sites, PSA provides comparable sizes of drug sites to those of canine serum albumin (CSA) which are larger than those of bovine, human and feline albumins. Such larger binding pockets can imply the ability of PSA to accommodate a broader spectrum of ligands. The findings here, especially the difference between BSA and PSA, can serve as a base to design effective biosensors to detect PSA contaminants.

Ractopamine (RAC) is a common β-agonist often used as a feed additive to improve muscle mass in farm animals. However, RAC has been banned in several countries due to its toxicity. To date, no clear evidence shows pharmacological and poisonous adverse effect of RAC in farm animals. In beef cattle, although RAC can be carried by bovine serum albumin (BSA) at drug site I, its effect on BSA structure and function remains unclear. Thus, in this work, Molecular Dynamics (MD) Simulations were employed to explore the binding interactions of RAC to BSA. Seemingly, RAC causes the high flexibility of domains I and III and importantly induces the large expansion of drug site II’s cavity which can interfere the drug-binding ability of drug site II. RAC binds to drug site I close to subdomain IIA, which is the same naproxen-binding site. Like naproxen, a polar moiety of RAC interacts with R194, R198 and W213. Our results reveal the RAC intrusion into the fatty acid site 6 (FA6) which implies the connection between drug site I and FA6 site. An insight into the RAC-BSA binding here can act as a base to better understand a drug distribution and bioavailability in cattle.

Human carnosinases (CNs) are dimeric dipeptidases in the metallopeptidase M20 family. Two isoforms of carnosinases (Zn²⁺‐containing carnosinase 1 (CN1) found in serum and Mn²⁺‐carnosinase 2 (CN2) in tissue) were identified. Both CNs cleave histidine‐containing (Xaa‐His) dipeptides such as carnosine where CN2 was found to accept a broader spectrum of substrates. A loss of CN function, resulting in a high carnosine concentration, reduces risk for diabetes and neurological disorders. Although several studies on CN activities and its Michaelis complex were conducted, all shed the light on CN1 activity where the CN2 data is limited. Also, the molecular details on CN1 and CN2 similarity and dissimilarity in structure and function remain unclear. Thus, in this work, molecular dynamics (MD) simulations were employed to study structure and dynamics of human CN1 and CN2 in comparison. The results show that the different catalytic ability of both CNs is due to their pocket size and environment. CN2 can accept a wider range of substrate due to the wider mouth of a binding pocket. The L1 loop seems to play a role in gating activity. Comparing to CN2, CN1 provides more electronegative entrance, more wettability, and higher stability of catalytic metal ion‐pair in the active site which allow more efficient water‐mediated catalysis. The microscopic understanding obtained here can serve as a basis for CN inhibition strategies resulting in higher carnosine levels and consequently mitigating complications associated with diseases such as diabetes and neurological disorder.

Human defensin 5 (HD5) is an antimicrobial peptide (AMP) with a broad-spectrum antimicrobial activity. Hence, it serves as a good candidate in AMP-derived antibiotic design. A substitution of E21 with arginine (E21R) and a second replacement of T7 with arginine (T7E21R) were found to enhance the antibacterial activity where the molecular insights into how these mutations enhance the bacteria-killing activity remains unclear. In this work, Molecular Dynamics (MD) simulations were employed to elucidate the binding mechanisms of both variants (E21R and T7E21R) on bacterial membrane. The dimaeric E21R shares similar adsorption mechanism to wildtype HD5 by using one chain to adhere to the bacterial membrane. In contrast, the more positively charged T7E21R employs both chains to bind to the membrane, resulting in greater membrane-binding ability. Nevertheless, the antibacterial activity of T7E21R is oligomeric state-independent. Both T7E21R monomer and dimer interact strongly with the membrane due to their high positive charges. Nonetheless, such high charges also hinder membrane translocation of the peptide. The positive charge of defensin-based antibiotics needs to be optimal to balance between their membrane-binding ability and their ability to translocate through bacterial membrane. This information serves as a useful guide for designing antimicrobial agents with membrane-disrupting function.

Malaria is a life-threatening disease in humans caused by Plasmodium parasites. Plasmodium vivax (P. vivax) is one of the prevalent species found worldwide. An increase in an anti-malarial drug resistance suggests the urgent need for new drugs. Zn²⁺-containing adenosine deaminase (ADA) is a promising drug target because the ADA inhibition is fatal to the parasite. Malarial ADA accepts both adenosine (ADN) and 5′-methylthioadenosine (MTA) as substrates. The understanding of the substrate binding becomes crucial for an anti-malarial drug development. In this work, ADA from P. vivax (pvADA) is of interest due to its prevalence worldwide. The binding of ADN and MTA are studied here using Molecular Dynamics (MD) simulations. Upon binding, the open and closed states of pvADA are captured. The displacement of α7, linking loops of β3/α12, β4/α13, β5/α15, and α10/α11 is involved in the cavity closure and opening. Also, the inappropriate substrate orientation induces a failure in a complete cavity closure. Interactions with D46, D172, S280, D310, and D311 are important for ADN binding, whereas only hydrogen bonds with D172 and D311 are sufficient to anchor MTA inside the pocket. No Zn²⁺-coordinated histidine residues is acquired for substrate binding. D172 is found to play a role in ribose moiety recognition, while D311 is crucial for trapping the amine group of an adenine ring towards the Zn²⁺ site. Comparing between ADN and MTA, the additional interaction between D310 and an amine nitrogen on ADN supports a tighter fit that may facilitate the deamination. Communicated by Ramaswamy H. Sarma

Human serum albumin (HSA) is abundant in blood. HSA binds a wide range of drugs, metabolites, and nutrients. A glycated HSA is also a potential diabetes biomarker. Recently, crystal structures of glucose- and fructose-bound HSA have been reported. Both cyclic and acyclic sugar forms are trapped in Sudlow site I. Galactose can also bind HSA, but no atomic detail is available. Thus, molecular dynamics simulations were employed to study the structural and dynamic properties of fructose- and galactose-bound HSA in comparison to glucose-bound HSA from previous studies. Both bound sugars promote different degrees of domain motions which can affect a drug/solute binding affinity at Sudlow site I. A large and highly water-exposed Sudlow site I allows high mobility of bound sugars. Nonetheless, more protein contacts imply a tighter binding of fructose than galactose. Although galactose and glucose are epimers, galactose forms a different interaction network which disrupts a formation of interactions with K195 and K199 resulting in the escape of galactose. In contrast, fructose molecules are anchored inside by a number of protein interactions and sugar dimer structure. These highlights the importance of protein–sugar and sugar–sugar interactions for ligand binding in large and highly water-exposed cavity.