Meng Fanwang

McMaster University | McMaster · Department of Chemistry and Chemical Biology

Molecular solubility is among the key properties that determine the clinical performance of a drug candidate because poor molecular solubility often indicates inadequate bioavailability. Using the CombiSolv-Exp database, we test several models (Gaussian process regression, decision trees, k-nearest neighbors) for hydration free energies by integrat...

Molecular solubility is among the key properties that determine the clinical performance of a drug candidate because poor molecular solubility often indicates inadequate bioavailability. Using the CombiSolv-Exp database, we test several models (Gaussian process regression, decision trees, k-nearest neighbors) for hydration free energies by integrat...

Post-translational modifications (PTMs) fine-tune various signaling pathways not only by the modification of a single residue, but also by the interplay of different modifications on residue pairs within or between proteins, defined as PTM cross-talk. As a challenging question, less attention has been given to PTM dynamics underlying cross-talk res...

Background: The volume of distribution at steady state (VDss) is a fundamental pharmacokinetics (PK) property of drugs, which measures how effectively a drug molecule is distributed throughout the body. Along with the clearance (CL), it determines the half-life and, therefore, the drug dosing interval. However, the molecular data size limits the ge...

Post-translational modification (PTM) is crucial for various cell signaling pathways and biological processes. However, the interactions between PTMs (PTM cross-talk) or PTMs and other sites (PTM mutation) are still in there infancy, with many challenges remaining unexplored. Since PTMs play a fundamental role in cell biology, many mutations cause...

Accurate prediction of post-translational modifications (PTMs) is of great significance in understanding cellular processes, by modulating protein structure and dynamics. Nowadays, with the rapid growth of protein data at different "omics" levels, machine learning models largely enriched the prediction of PTMs. However, most machine learning models...

We have developed Procrustes, a free, open-source, cross-platform, and user-friendly Python library implementing a wide-range of algorithmic solutions to Procrustes problems. The goal of Procrustes analysis is to find an optimal transformation that makes two matrices as close as possible to each other, where the matrices are often (but need not alw...

The highly-selective blood-brain barrier (BBB) prevents neurotoxic substances in blood from crossing into the extracellular fluid of the central nervous system (CNS). As such, the BBB has a close relationship with CNS disease development and treatment, so predicting whether a substance crosses the BBB is a key task in lead discovery for CNS drugs....

p>Novel therapies that enhance ADCC have the potential to overcome Rituximab (RTX) resistance in lymphoma, which can occur due to e.g. CD20 loss, immunogenicity-induced reduction in RTX exposure, or SNPs resulting in lower CD16:Fc affinity. Nonlinear interactions between effector cells (ECs), drug, and target cell (TC) factors in ADCC, however, com...

IOData is a free and open‐source Python library for parsing, storing, and converting various file formats commonly used by quantum chemistry, molecular dynamics, and plane‐wave density‐functional‐theory software programs. In addition, IOData supports a flexible framework for generating input files for various software packages. While designed and r...

Modern drug design aims to discover novel lead compounds with attractable chemical profiles to enable further exploration of the intersection of chemical space and biological space. Identification of small molecules with good ligand efficiency, high activity, and selectivity is crucial toward developing effective and safe drugs. However, the inters...

Background: As a traditional Chinese herb, safflower (Carthamus tinctorius L.) is valued for its florets to prevent cardiovascular and cerebrovascular diseases. Basing on previous chemical analysis, the main active compounds are flavonoids in its florets. Although flavonoid biosynthetic pathway has been well-documented in many model species, uniqu...

Elucidating the conformational heterogeneity of proteins is essential for understanding protein function and developing exogenous ligands. With the rapid development of experimental and computational methods, it is of great interest to integrate these approaches to illuminate the conformational landscapes of target proteins. SETD8 is a protein lysi...

Background: On a tide of big data machine learning is coming to its day. Referring to huge amounts of epigenetic data coming from biological experiments and clinic, machine learning can help in detecting epigenetic features in genome, finding correlations between phenotypes and modifications in histone or genes, accelerating the screen of lead com...

Elucidating conformational heterogeneity of proteins is essential for understanding protein functions and developing exogenous ligands for chemical perturbation. While structural biology methods can provide atomic details of static protein structures, these approaches cannot in general resolve less populated, functionally relevant conformations and...

SET7, serving as the only histone methyltransferase that monomethylates 'Lys-4' of histone H3, has been proved to function as a key regulator in diverse biological processes, such as cell proliferation, transcriptional network regulation in embryonic stem cell, cell cycle control, protein stability, heart morphogenesis and development. What's more,...

Epigenetic modifying enzymes have been proven to play significant roles in gene regulation and cancer pathogenesis. As the star targets both in academic and industrial fields, epigenetic targets have been extensively studied and several epigenetic inhibitors have been proven for the treatment of cancer. However, the identification of epigenetic tar...

Histone methyltransferases are involved in many important biological processes, and abnormalities in these enzymes are associated with tumorigenesis and progression. Disruptor of telomeric silencing 1-like (DOT1L), a key hub in histone lysine methyltransferases, has been reported to play an important role in the processes of mixed lineage leukemia...

Two new alkaloids, plantadeprate A (1) and 1'-(4″-hydroxybutyl)plantagoguanidinic acid (2), along with three known compounds, were isolated from the seeds of Plantago depressa. Their structures were elucidated by physical data analyses including NMR, MS, and electronic circular dichroism (ECD) methods. Plantadeprate A (1), a monoterpene zwitterioni...

Histone methyltransferases are involved in various biological functions, and these methylation regulating enzymes abnormal expression or activity has been noted in several human cancers. Within this context, SET domain-containing (lysine methyltransferase) 7 (SET7, also called KMT7, SETD7, SET9) is of increasing significance due to its diverse role...

Three new chalcones, xanthoangelols K–M (1–3), together with 19 known compounds were isolated from the stems of Angelica keiskei Koidzumi, a well-known rejuvenated and anti-diabetic plant originated from Japan. The structures of compounds 1–3 were elucidated on the basis of spectroscopic data and Mosher’s method. All compounds were evaluated for th...

To discriminate the fruits of Ziziphus jujuba and Z. jujuba var. spinosa, a binary detector fingerprint was proposed and validated by utilizing HPLC coupled with two detection techniques of diode assay detection (DAD) and evaporative light scattering detection (ELSD). Using the data fusion method, the two sets of chromatographic data were combined...