Mohammad Hassan Baig

Computer Aided Drug Design: Success and Limitations.

Over the last few decades, computer-aided drug design has emerged as a powerful technique playing a crucial role in the development of new drug molecules. Structure-based drug design and ligand-based drug design are two methods commonly used in computer-aided drug design. In this article, we discuss the theory behind both methods, as well as their successful applications and limitations. To accomplish this, we reviewed structure based and ligand based virtual screening processes. Molecular dynamics simulation, which has become one of the most influential tool for prediction of the conformation of small molecules and changes in their conformation within the biological target, has also been taken into account. Finally, we discuss the principles and concepts of molecular docking, pharmacophores and other methods used in computer-aided drug design.

Biophysical Study on the Interaction between Eperisone Hydrochloride and Human Serum Albumin Using Spectroscopic, Calorimetric, and Molecular Docking Analyses

Eperisone hydrochloride (EH) is widely used as a muscle relaxant for patients with muscular contracture, low back pain, or spasticity. Human serum albumin (HSA) is a highly soluble negatively charged, endogenous and abundant plasma protein ascribed with the ligand binding and transport properties. The current study was undertaken to explore the interaction between EH and the serum transport protein, HSA. Study of the interaction between HSA and EH was carried by UV-vis, fluorescence quenching, circular dichroism (CD), Fourier transform infrared (FTIR) spectroscopy, Försters resonance energy transfer, isothermal titration calorimetry and differential scanning calorimetry. Tryptophan fluorescence intensity of HSA was strongly quenched by EH. The binding constants (Kb) were obtained by fluorescence quenching, and results show that the HSA-EH interaction revealed a static mode of quenching with binding constant Kb ≈ 104 reflecting high affinity of EH for HSA. The negative ΔG° value for binding indicated that HSA-EH interaction was a spontaneous process. Thermodynamic analysis shows HSA-EH complex formation occurs primarily due to hydrophobic interactions, and hydrogen bonds were facilitated at the binding of EH. EH binding induces α-helix of HSA as obtained by far-UV CD and FTIR spectroscopy. In addition, the distance between EH (acceptor) and Trp residue of HSA (donor) was calculated 2.18 nm using Försters resonance energy transfer theory. Furthermore, molecular docking results revealed EH binds with HSA, and binding site was positioned in Sudlow Site I of HSA (subdomain IIA). This work provides a useful experimental strategy for studying the interaction of myorelaxant with HSA, helping to understand the activity and mechanism of drug binding.

Binding of erucic acid with human serum albumin using a spectroscopic and molecular docking study

Erucic acid (EA) is one of the key fatty acids usually found in canola oil, mustard oil and rapeseed oil. Consumption of EA in primates was found to cause myocardial lipidosis and cardiac steatosis. To have an insight of the effect of EA in humans, we performed in vitro interaction studies of EA with the primary plasma protein, human serum albumin (HSA). Spectroscopic (UV-vis and fluorescence) analysis of the HSA-EA interaction revealed a static mode of quenching with binding constant Kb ∼104 reflecting high affinity of EA for HSA. The negative value of ΔG° for binding of EA to HSA in the fluorescence studies indicates the process to be spontaneous. Thermodynamic signatures of the HSA-EA interaction in the complex reflect dominance of hydrogen bonds. Despite predominance of hydrogen bonds, hydrophobic interactions in the HSA-EA complex were found acting as a contributing factor in the binding of EA to HSA, observed as structural change in the far-UV CD spectra. Försters resonance energy transfer of the EA-HSA complex revealed a distance of 3.2nm between acceptor molecules (EA) and the donor Trp residue of HSA. To have a deeper insight of the structural dependence of the HSA-EA interaction in the complex, thermodynamic study was supplemented with molecular docking. The molecular docking analysis further highlighted the EA binding in the subdomain IIIA (Sudlow site II) of HSA. The information generated in the study reflects greater pharmacological significance of EA and highlights its importance in the clinical medicine.

Fibromodulin: a master regulator of myostatin controlling progression of satellite cells through a myogenic program

Differentiation of muscle satellite cells (MSCs) involves interaction of the proteins present in the extracellular matrix (ECM) with MSCs to regulate their activity, and therefore phenotype. Herein, we report fibromodulin (FMOD), a member of the proteoglycan family participating in the assembly of ECM, as a novel regulator of myostatin (MSTN) during myoblast differentiation. In addition to having a pronounced effect on the expression of myogenic marker genes [myogenin (MYOG) and myosin light chain 2 (MYL2)], FMOD was found to maintain the transcriptional activity of MSTN. Moreover, coimmunoprecipitation and in silico studies performed to investigate the interaction of FMOD helped confirm that it antagonizes MSTN function by distorting its folding and preventing its binding to activin receptor type IIB. Furthermore, in vivo studies revealed that FMOD plays an active role in healing by increasing satellite cell recruitment to sites of injury. Together, these findings disclose a hitherto unrecognized regulatory role for FMOD in MSCs and highlight new mechanisms whereby FMOD circumvents the inhibitory effects of MSTN and triggers myoblast differentiation. These findings offer a basis for the design of novel MSTN inhibitors that promote muscle regeneration after injury or for the development of pharmaceutical agents for the treatment of different muscle atrophies.—Lee, E. J., Jan, A. T., Baig M. H., Ashraf, J. M., Nahm, S.‐S., Kim, Y.‐W., Park, S.‐Y., Choi, I. Fibromodulin: a master regulator of myostatin controlling progression of satellite cells through a myogenic program. FASEB J. 30, 2708‐2719 (2016). www.fasebj.org

Broad-spectrum inhibition of AHL-regulated virulence factors and biofilms by sub-inhibitory concentrations of ceftazidime

Quorum sensing (QS) in bacteria is a density dependent communication system that regulates the expression of genes, including production of virulence factors in many pathogens. The emergence of antibiotic resistance among pathogenic bacteria represents a major threat in both hospitals as well as environmental settings. Interference of quorum sensing (QS)-regulated virulence factors and biofilms is a recognized anti-pathogenic therapy. Safe, stable and effective anti-QS agents are needed to combat diseases caused by multidrug-resistant bacteria. The present study was performed to assess the inhibitory effect of third generation antibiotic ceftazidime against Gram-negative bacterial pathogens. Sub-MICs of ceftazidime demonstrated dose dependent inhibition of QS regulated virulence traits and biofilm formation in various strains of Chromobacterium violaceum (CV12472 and CVO26), Pseudomonas aeruginosa (PAO1 and PAF79) and Aeromonas hydrophila (WAF38). β-galactosidase assay revealed ceftazidime inhibited the las and pqs QS systems in P. aeruginosa. Alongside, in vivo studies demonstrated enhanced survival of Caenorhabditis elegans after the treatment with the drug. Molecular docking analysis showed the high binding affinity of ceftazidime which represents its QS inhibitory activity. By highlighting the broad spectrum anti-quorum sensing and biofilm inhibiting activities against 3 different bacterial pathogens, ceftazidime seems a more potent candidate in counteracting the infections caused by drug resistant bacteria.

Eugenol inhibits quorum sensing and biofilm of toxigenic MRSA strains isolated from food handlers employed in Saudi Arabia

ABSTRACT Food handlers are important component in assessment and maintenance of food quality as they are carriers of food pathogens causing spoilage. Food spoilage is attributed to quorum sensing (QS) controlled development of biofilms. Therefore, there is an urgent need to develop novel QS and biofilm inhibitors to prevent spoilage of food products. In the present study, toxin producing biofilm forming methicillin-resistant Staphylococcus aureus (MRSA) were isolated from food handlers. Further, eugenol was screened for its QS and anti-biofilm properties. Analysis of nasal and hand swabs revealed the presence of seven toxigenic and biofilm forming MRSA strains. Eugenol demonstrated significant anti-QS activity in CVO26 and also reduced the QS-regulated production of elastase, protease, chitinase, pyocyanin and exopolysaccharide (EPS) in PAO1 considerably. Eugenol demonstrated 17%–86%, 24%–69%, 30%–91%, 9%–94% and 4%–89% reduction in biofilm biomass of S. aureus ATCC 25923 and MRSA strains FSA3, FSA11, FSA13 and FSA32, respectively. Sub-inhibitory concentrations of eugenol also decreased the metabolic activity in biofilm cells. Molecular docking analysis showed high binding affinity of eugenol that represents its biofilm inhibitory activity. This is the first report on the carriage of toxigenic drug-resistant biofilm forming S. aureus by food handlers and inhibition of their biofilms in the Kingdom of Saudi Arabia. The findings give a clear insight into the food safety hazards associated with the carriage of S. aureus and present eugenol as a broad-spectrum anti-QS and anti-biofilm agent.

Identification of Potent Caspase-3 Inhibitors for Treatment of Multi- Neurodegenerative Diseases Using Pharmacophore Modeling and Docking Approaches

Neurodegenerative disorders are due to excessive neuronal apoptosis and the caspase-3 plays a key role in the apoptotic pathway. The caspase-3 inhibition may be a validated therapeutic approach for neurodegenerative disorders and an interesting target for molecular modeling studies using both Ligand and structure based approaches. In view of the above we have generated the Ligand based pharmacophore model using the Discovery studio 2.0 software. In addition to this a structure based approach has been used to validate the developed pharmacophoric features to gain a deeper insight into its molecular recognition process. This validated pharmacophore and the docking model was then implemented as a query for pharmacophore based virtual screening to prioritize the probable hits for the Caspase-3. Two ligands, ZINC12405015 and ZINC12405043 were finally selected on the basis of their fit values and docking scores. This study also reveals the important amino acids viz. His-121, Ser-205, Arg-207 which were found to be playing crucial role in the binding of the selected compounds within the active site of caspase-3.

Fibromodulin and regulation of the intricate balance between myoblast differentiation to myocytes or adipocyte-like cells

Interactions between myoblasts and the surrounding microenvironment led us to explore the role of fibromodulin (FMOD), an extracellular matrix protein, in the maintenance of myoblast stemness and function. Microarray analysis of FMODkd myoblasts and in silico studies were used to identify the top most differentially expressed genes in FMODkd, and helped establish that FMOD‐based regulations of integral membrane protein 2a and clusterin are essential components of the myogenic program. Studies in knockout, obese, and diabetic mouse models helped characterize the operation of a novel FMOD‐based regulatory circuit that controls myoblast switching from a myogenic to a lipid accumulation fate. FMOD regulation of myoblasts is an essential part of the myogenic program, and it offers opportunities for the development of therapeutics for the treatment of different muscle diseases.—Lee, E. J., Jan, A. T., Baig, M. H., Ahmad, K., Malik, A., Rabbani, G., Kim, T., Lee, I.‐K., Lee, Y. H., Park, S.‐Y., Choi, I. Fibromodulin and regulation of the intricate balance between myoblast differentiation to myocytes or adipocyte‐like cells. FASEB J. 32, 768–781 (2018). www.fasebj.org

Commonalities in Biological Pathways, Genetics, and Cellular Mechanism between Alzheimer Disease and Other Neurodegenerative Diseases: An in Silico-updated Overview

BACKGROUND Alzheimers disease (AD) is the most common and well-studied neurodegenerative disease (ND). Biological pathways, pathophysiology and genetics of AD show commonalities with other NDs viz. Parkinsons disease (PD), Amyotrophic lateral sclerosis (ALS), Huntingtons disease (HD), Prion disease and Dentatorubral-pallidoluysian atrophy (DRPLA). Many of the NDs, sharing the common features and molecular mechanisms suggest that pathology may be directly comparable and be implicated in disease prevention and development of highly effective therapies. METHOD In this review, a brief description of pathophysiology, clinical symptoms and available treatment of various NDs have been explored with special emphasis on AD. Commonalities in these fatal NDs provide support for therapeutic advancements and enhance the understanding of disease manifestation. CONCLUSION The studies concentrating on the commonalities in biological pathways, cellular mechanisms and genetics may provide the scope to researchers to identify few novel common target(s) for disease prevention and development of effective common drugs for multi-neurodegenerative diseases.

Binding of Tolperisone Hydrochloride with Human Serum Albumin: Effects on the Conformation, Thermodynamics, and Activity of HSA

Tolperisone hydrochloride (TH) has muscle relaxant activity and has been widely used for several years in clinical practice to treat pathologically high skeletal muscle tone (spasticity) and related pains. The current study was designed to explore the binding efficacy of TH with human serum albumin (HSA) using multispectrscopic, calorimetric approach, FRET, esterase-like activity, and a molecular docking method. A reduction in fluorescence emission at 340 nm of HSA was attributed to fluorescence quenching by TH via a static quenching type. Binding constants ( Kb) were evaluated at different temperatures, and obtained Kb values were ∼104 M-1, which demonstrated moderately strong affinity of TH for HSA. A calculated negative Δ G° value indicated spontaneous binding of TH to HSA. Far-UV CD spectroscopy revealed that the α-helix content was increased after TH binding. The binding distance between donor and acceptor was calculated to be 2.11 nm based on Försters resonance energy transfer theory. ITC results revealed TH interacted with HSA via hydrophobic interactions and hydrogen bonding. The thermal stability of HSA was studied using DSC, and results showed that in the presence of TH the structure of HSA was significantly more thermostable. The esterase-like activity of HSA showed fixed Vmax and increased Km suggesting that TH binds with HSA in a competitive manner. Furthermore, molecular docking results revealed TH binds in the cavity of HSA, that is, subdomain IIA (Sudlow site I), and that it hydrogen bonds with K199 and H242 of HSA. Binding studies of drugs with HSA are potentially useful for elucidating chemico-biological interactions that can be utilized in the drug design, pharmaceutical, pharmacology, and biochemistry fields. This extensive study provides additional insight of ligand binding and structural changes induced in HSA relevant to the biological activity of HSA in vivo.