Computational drug discovery of an inhibitor of APOBEC3B as a treatment for epithelial cancers.

Cancer is one of the leading causes of death in the U.S., and tumorous cancers such as cervical, lung, breast, and ovarian cancers are the most common types. APOBEC3B is a nonessential cytidine deaminase found in humans and theorized to defend against viral infection. However, overexpression of APOBEC3B is linked to cancer in humans, which makes APOBEC3B a potential cancer treatment target through competitive inhibition for several tumorous cancers. Computational studies can help reveal a small molecule inhibitor using high-throughput virtual screening of millions of candidates with relatively little cost. This study aims to narrow the field of potential APOBEC3B inhibition candidates for future in vitro assays and provide an effective scaffold for drug design studies. Another goal of this project is to provide critical amino acid targets in the active site for future drug design studies. This study simulated 7.8 million drug candidates using high-throughput virtual screening and further processed the top scoring 241 molecules from AutoDock Vina, DOCK 6, and de novo design. Using virtual screening, de novo design, and molecular dynamics simulations, a competitive inhibitor candidate was discovered with an average binding free energy score of -46.03 kcal/mol, more than 10 kcal/mol better than the substrate control (dCMP). These results indicate that this molecule (or a structural derivative) may be an effective inhibitor of APOBEC3B and prevent host genome mutagenesis resulting from protein overexpression. Another important finding is the confirmation of essential amino acid targets, such as Tyr250 and Gln213 within the active site of APOBEC3B. Therefore, study used novel computational methods to provide a theoretical scaffold for future drug design studies that may prove useful as a treatment for epithelial cancers.Communicated by Ramaswamy H. Sarma.

Exploring the disruption of SARS-CoV-2 RBD binding to hACE2.

The COVID-19 pandemic was declared due to the spread of the novel coronavirus, SARS-CoV-2. Viral infection is caused by the interaction between the SARS-CoV-2 receptor binding domain (RBD) and the human ACE2 receptor (hACE2). Previous computational studies have identified repurposed small molecules that target the RBD, but very few have screened drugs in the RBD-hACE2 interface. When studies focus solely on the binding affinity between the drug and the RBD, they ignore the effect of hACE2, resulting in an incomplete analysis. We screened ACE inhibitors and previously identified SARS-CoV-2 inhibitors for binding to the RBD-hACE2 interface, and then conducted 500 ns of unrestrained molecular dynamics (MD) simulations of fosinopril, fosinoprilat, lisinopril, emodin, diquafosol, and physcion bound to the interface to assess the binding characteristics of these ligands. Based on MM-GBSA analysis, all six ligands bind favorably in the interface and inhibit the RBD-hACE2 interaction. However, when we repeat our simulation by first binding the drug to the RBD before interacting with hACE2, we find that fosinopril, fosinoprilat, and lisinopril result in a strongly interacting trimeric complex (RBD-drug-hACE2). Hydrogen bonding and pairwise decomposition analyses further suggest that fosinopril is the best RBD inhibitor. However, when lisinopril is bound, it stabilizes the trimeric complex and, therefore, is not an ideal potential drug candidate. Overall, these results reveal important atomistic interactions critical to the binding of the RBD to hACE2 and highlight the significance of including all protein partners in the evaluation of a potential drug candidate.

Risk Factors Associated With Neurological and Extra-Neurological Complications and Mortality in Patients With Stroke.

Introduction Understanding when and how systemic complications can occur after an acute stroke is crucial. It is important to identify patients who are at higher risk for these complications. Early and effective treatment based on this knowledge can significantly improve patient outcomes. The objective of this study was to identify the risk factors associated with neurological and extra-neurological complications and mortality in stroke patients treated at a secondary care hospital. Methods Of a total of 170 patients diagnosed with hemorrhagic/ischemic stroke and transient cerebral ischemia at a secondary care hospital in Mexico, the records of 125 were reviewed and of these, 86 were included in the study. The study group comprised 86 adult patients (> 18 years of age) diagnosed with ischemic or hemorrhagic stroke or transient cerebral ischemia. Their demographics, clinical characteristics, in-hospital complications, and mortality were retrospectively analyzed.  Results Of the 86 patients examined, 34.9% experienced complications, regardless of the type of stroke. The most significant factor associated with mortality and complications during hospitalization in patients with stroke was previous diseases. Other factors that were linked to higher mortality were pre-existing medical conditions. The most common neurological complication among patients with stroke during hospitalization was intracranial hypertension (3.5%). As for extra-neurological complications, pressure ulcers and nosocomial pneumonia had an occurrence rate of 4.7%. Conclusions The main neurological complication during hospitalization of patients with stroke was intracranial hypertension, while the extra neurological complications were pressure ulcers and nosocomial pneumonia.

Spontaneous Intracranial Hemorrhage Associated With an Intracranial Meningioma.

Spontaneous intracranial hemorrhage associated with an intracranial meningioma is rare, with a reported incidence of below 2.4% of all meningiomas. Such cases are described with a cause subdural with intratumoral hemorrhage, which is a challenge for patients and healthcare professionals because it can occur spontaneously without other pathological antecedents. We describe the case of a 55-year-old woman with subdural hemorrhage over the frontoparietal region of the right hemisphere associated with a meningioma, generating a mass effect and shifting the third ventricle and lateral ventricle. Therefore, urgent surgical treatment was decided. A tumor lesion was found with apoplexy, soft consistency, and violaceous color with abundant vascularity in the lesion's center, suggesting a probable angiomatous meningioma. The histopathological evaluation confirmed meningothelial hemorrhagic meningioma grade I, according to the World Health Organization grading. This article discusses the causes, risk factors, diagnosis, and surgical treatment for hemorrhage associated with intracranial meningioma.

Visceral leishmaniasis (kala-azar) caused by L. mexicana in a patient with AIDS.

We describe a patient with HIV who presented with hemophagocytic lymphohistiocytosis and nonspecific abdominal imaging findings. He was diagnosed with visceral leishmaniasis via bone marrow biopsy and treated in the hospital with amphotericin B infusions. Despite pharmacologic interventions, including amphotericin and miltefosine in addition to antiretroviral therapy, our patient experienced multiple relapses and a challenging clinical course.

Alleles of unc-33/CRMP exhibit defects during Caenorhabditis elegans epidermal morphogenesis.

BACKGROUND: Microtubule-associated proteins regulate the dynamics, organization, and function of microtubules, impacting a number of vital cellular processes. CRMPs have been shown to control microtubule assembly and axon outgrowth during neuronal differentiation. While many microtubule-associated proteins have been linked to roles in cell division and neuronal development, it is still unclear the complement that control the formation of parallel microtubule arrays in epithelial cells. RESULTS: Here we show through time-lapse DIC microscopy that Caenorhabditis elegans embryos homozygous for the weak loss-of-function allele unc-33(e204) progress more slowly through epidermal morphogenesis, while animals homozygous for strong loss-of-function alleles exhibit more embryonic lethality. Identification of two novel missense mutations in unc-33(e572), Val476Gly, and Ser731Thr, lead to computational approaches to determine the potential effects of these changes on UNC-33/CRMP structure. Molecular dynamics simulations show that for Asp389Asn and Arg502His, two other known missense mutations, local changes in protein-protein hydrogen bonding affect the stability of the protein. However, the Val476Gly/Ser731Thr combination does not alter the structure or energetics of UNC-33 drastically when compared to the wild-type protein. CONCLUSIONS: These results support a novel role for UNC-33/CRMP in C. elegans epidermal development and shed light on how individual amino acid changes cause a loss-of-function in UNC-33.

Enhanced Photoacoustic Detection of Heparin in Whole Blood via Melanin Nanocapsules Carrying Molecular Agents.

Photoacoustic (PA) imaging has proved versatile for many biomedical applications from drug delivery tracking to disease diagnostics and postoperative surveillance. It recently emerged as a tool for accurate and real-time heparin monitoring to avoid bleeding complications associated with anticoagulant therapy. However, molecular-dye-based application is limited by high concentration requirements, photostability, and a strong background hemoglobin signal. We developed polydopamine nanocapsules (PNCs) via supramolecular templates and loaded them with molecular dyes for enhanced PA-mediated heparin detection. Depending on surface charge, the dye-loaded PNCs undergo disassembly or aggregation upon heparin recognition: both experiments and simulation have revealed that the increased PA signal mainly results from dye-loaded PNC-heparin aggregation. Importantly, Nile blue (NB)-loaded PNCs generated a 10-fold higher PA signal than free NB dye, and such PNC enabled the direct detection of heparin in a clinically relevant therapeutic window (0-4 U/mL) in whole human blood (R2 = 0.91). Furthermore, the PA signal of PNC@NB obtained from 17 patients linearly correlated with ACT values (R2 = 0.73) and cumulative heparin (R2 = 0.83). This PNC-based strategy for functional nanocapsules offers a versatile engineering platform for robust biomedical contrast agents and nanocarriers.

Mechanisms of allosteric and mixed mode aromatase inhibitors.

Aromatase (CYP19) catalyzes the last biosynthetic step of estrogens in mammals and is a primary drug target for hormone-related breast cancer. However, treatment with aromatase inhibitors is often associated with adverse effects and drug resistance. In this study, we used virtual screening targeting a predicted cytochrome P450 reductase binding site on aromatase to discover four novel non-steroidal aromatase inhibitors. The inhibitors have potencies comparable to the noncompetitive tamoxifen metabolite, endoxifen. Our two most potent inhibitors, AR11 and AR13, exhibit both mixed-type and competitive-type inhibition. The cytochrome P450 reductase-CYP19 coupling interface likely acts as a transient binding site. Our modeling shows that our inhibitors bind better at different sites near the catalytic site. Our results predict the location of multiple ligand binding sites on aromatase. The combination of modeling and experimental results supports the important role of the reductase binding interface as a low affinity, promiscuous ligand binding site. Our new inhibitors may be useful as alternative chemical scaffolds that may show different adverse effects profiles than current clinically used aromatase inhibitors.

Biflavonoid-Induced Disruption of Hydrogen Bonds Leads to Amyloid-ß Disaggregation.

Deposition of amyloid ß (Aß) fibrils in the brain is a key pathologic hallmark of Alzheimer's disease. A class of polyphenolic biflavonoids is known to have anti-amyloidogenic effects by inhibiting aggregation of Aß and promoting disaggregation of Aß fibrils. In the present study, we further sought to investigate the structural basis of the Aß disaggregating activity of biflavonoids and their interactions at the atomic level. A thioflavin T (ThT) fluorescence assay revealed that amentoflavone-type biflavonoids promote disaggregation of Aß fibrils with varying potency due to specific structural differences. The computational analysis herein provides the first atomistic details for the mechanism of Aß disaggregation by biflavonoids. Molecular docking analysis showed that biflavonoids preferentially bind to the aromatic-rich, partially ordered N-termini of Aß fibril via the π-π interactions. Moreover, docking scores correlate well with the ThT EC50 values. Molecular dynamic simulations revealed that biflavonoids decrease the content of ß-sheet in Aß fibril in a structure-dependent manner. Hydrogen bond analysis further supported that the substitution of hydroxyl groups capable of hydrogen bond formation at two positions on the biflavonoid scaffold leads to significantly disaggregation of Aß fibrils. Taken together, our data indicate that biflavonoids promote disaggregation of Aß fibrils due to their ability to disrupt the fibril structure, suggesting biflavonoids as a lead class of compounds to develop a therapeutic agent for Alzheimer's disease.

Understanding the Structure and Apo Dynamics of the Functionally Active JIP1 Fragment.

Recent experiments indicate that the C-Jun amino-terminal kinase-interacting protein 1 (JIP1) binds to and activates the c-Jun N-terminal kinase (JNK) protein. JNK is an integral part of cell apoptosis, and misregulation of this process is a causative factor in diseases such as Alzheimer's disease (AD), obesity, and cancer. It has also been shown that JIP1 may increase the phosphorylation of tau by facilitating the interaction between the tau protein and JNK, which could also be a causative factor in AD. Very little is known about the structure and dynamics of JIP1; however, the amino acid composition of the first 350 residues suggests that it contains an intrinsically disordered region. Molecular dynamics (MD) simulations using AMBER 14 were used to study the structure and dynamics of a functionally active JIP1 10mer fragment to better understand the solution behavior of the fragment. Two microseconds of unbiased MD was performed on the JIP1 10mer fragment in 10 different seeds for a total of 20 µs of simulation time, and from this, seven structurally stable conformations of the 10mer fragment were identified via classical clustering. The 10mer ensemble was also used to build a Markov state model (MSM) that identified four metastable states that encompassed six of the seven conformational families identified by classical dimensional reduction. Based on this MSM, conformational interconversions between the four states occur via two dominant pathways with probability fluxes of 55 and 44% for each individual pathway. Transitions between the initial and final states occur with mean first passage times of 31 (forward) and 16 (reverse) µs.

Psychological Constructs Related to Seat Belt Use: A Nationally Representative Survey Study.

Seat belt use can significantly reduce fatalities in motor vehicle crashes (Kahane, 2000). Nevertheless, the current U.S. seat belt use rate of 89.6% (Enriquez & Pickrell, 2019) indicates that a relatively small but pervasive portion of the population does not wear seat belts on a full-time basis. Whereas much is known about the demographic predictors of seat belt use, far less is understood about psychological factors that predict individual proclivities toward using or not using a seat belt. In this study, we examined some of these potential psychological predictors. A probability-based web survey was conducted with 6,038 U.S. residents aged 16 or older who reported having driven or ridden in a car in the past year. We measured self-reported seat belt use and 18 psychological constructs and found that delay of gratification, life satisfaction, risk aversion, risk perception, and resistance to peer influence were positively associated with belt use. Impulsivity and social resistance orientation were negatively associated with belt use. Prior research has shown that psychological factors like delay of gratification, risk aversion/perception, and impulsivity predict other health behaviors (e.g., cigarette smoking, sunscreen use); our results extend this literature to seat belts and can aid the development of traffic safety programs targeted at non-users who-due to such factors-may be resistant to more traditional countermeasures such as legislation and enforcement.

Novel Noncompetitive Type Three Secretion System ATPase Inhibitors Shut Down Shigella Effector Secretion.

Shigella is the causative agent of bacillary dysentery and is responsible for an estimated 165 million infections and 600,000 deaths annually. Like many Gram-negative pathogens, Shigella relies on a type three secretion system (T3SS) to initiate and sustain infection by directly injecting effector proteins into host cells. Protein secretion through the needle-like injectisome and overall Shigella virulence rely on the T3SS ATPase Spa47, making it a likely means for T3SS regulation and an attractive target for therapeutic small molecule inhibitors. Here, we utilize a recently solved 2.15 Å crystal structure of Spa47 to computationally screen 7.6 million drug-like compounds for candidates which avoid the highly conserved active site by targeting a distal, but critical, interface between adjacent protomers of the Spa47 homohexamer. Ten of the top inhibitor candidates were characterized, identifying novel Spa47 inhibitors that reduce in vitro ATPase activity by as much as 87.9 ± 10.5% with IC50's as low as 25 ± 20 µM and reduce in vivo Shigella T3SS protein secretion by as much as 94.7 ± 3.0%. Kinetic analyses show that the inhibitors operate through a noncompetitive mechanism that likely supports the inhibitors' low cytotoxicity, as they avoid off-target ATPases involved in either Shigella or mammalian cell metabolism. Interestingly, the inhibitors display nearly identical inhibition profiles for Spa47 and the T3SS ATPases EscN from E. coli and FliI from Salmonella. Together, the results of this study provide much-needed insight into T3SS ATPase inhibition mechanisms and a strong platform for developing broadly effective cross-pathogen T3SS ATPase inhibitors.

A Mechanistic Investigation of Methylene Blue and Heparin Interactions and Their Photoacoustic Enhancement.

We recently reported a real-time method to measure heparin in human whole blood based on the photoacoustic change of methylene blue (MB). Intriguingly, the MB behaved unlike other "turn on" photoacoustic probes-the absorbance decreased as the photoacoustic signal increased. The underlying mechanism was not clear and motivated this study. We studied the binding mechanism of MB and heparin in water and phosphate buffer saline (PBS) with both experimental and computational methods. We found that the photoacoustic enhancement of the MB-heparin mixture was a result of MB-heparin aggregation due to charge neutralization and resulting sequestration of MB in these aggregates. The sequestration of MB in the MB-heparin aggregates led to decreased absorbance-there was simply less free dye in solution to absorb light. The highest photoacoustic signal and aggregation occurred when the number of negatively charged sulfate groups on heparin was approximately equal to the number of positively charged MB molecule. The MB-heparin aggregates dissociated when there were more sulfated groups from heparin than MB molecules because of the electrostatic repulsion between negatively charged sulfate groups. PBS facilitated MB dimer formation regardless of heparin concentration and reprecipitated free MB in aggregates due to ionic strength and ionic shielding. Further molecular dynamics experiments found that binding of heparin occurred at the sulfates and glucosamines in heparin. Phosphate ions could interact with the heparin via sodium ions to impair the MB-heparin binding. Finally, our model found 3.7-fold more MB dimerization upon addition of heparin in MB solution confirming that heparin facilitates MB aggregation. We conclude that the addition of heparin in MB decreases the absorbance of the sample because of MB-heparin aggregation leading to fewer MB molecules in solution; however, the aggregation also increases the PA intensity because the MB molecules in the MB-heparin aggregate have reduced degrees of freedom and poor heat transfer to solvent.

Nasal Cannula Apneic Oxygenation Prevents Desaturation During Endotracheal Intubation: An Integrative Literature Review.

Patients requiring emergency airway management may be at greater risk of acute hypoxemic events because of underlying lung pathology, high metabolic demands, insufficient respiratory drive, obesity, or the inability to protect their airway against aspiration. Emergency tracheal intubation is often required before complete information needed to assess the risk of procedural hypoxia is acquired (i.e., arterial blood gas level, hemoglobin value, or chest radiograph). During pre-oxygenation, administering high-flow nasal oxygen in addition to a non-rebreather face mask can significantly boost the effective inspired oxygen. Similarly, with the apnea created by rapid sequence intubation (RSI) procedures, the same high-flow nasal cannula can help maintain or increase oxygen saturation during efforts to secure the tube (oral intubation). Thus, the use of nasal oxygen during pre-oxygenation and continued during apnea can prevent hypoxia before and during intubation, extending safe apnea time, and improve first-pass success attempts. We conducted a literature review of nasal-cannula apneic oxygenation during intubation, focusing on two components: oxygen saturation during intubation, and oxygen desaturation time. We performed an electronic literature search from 1980 to November 2017, using PubMed, Elsevier, ScienceDirect, and EBSCO. We identified 14 studies that pointed toward the benefits of using nasal cannula during emergency intubation.

Investigation of Nascent Base Pair and Polymerase Behavior in the Presence of Mismatches in DNA Polymerase I Using Molecular Dynamics.

Optimizing DNA polymerases for a broad range of tasks requires an understanding of the factors influencing polymerase fidelity, but many details of polymerase behavior remain unknown, especially in the presence of mismatched nascent base pairs. Using molecular dynamics, the large fragment of Bacillus stearothermophilus DNA polymerase I is simulated in the presence of all 16 possible standard nucleoside triphosphate-template (dNTP-dN) pairs, including four Watson-Crick pairs and 12 mismatches. The precatalytic steps of nucleotide addition from nucleotide insertion to immediately preceding catalysis are explored using three starting structures representing different stages of nucleotide addition. From these simulations, interactions between dNTPs and the DNA-protein complex formed by the polymerase are elucidated. Patterns of large-scale conformational shifts, classification of nucleotide pairs based on composition, and investigation of the roles of residues interacting with dNTPs are completed on 50+ µs of simulation. The role of molecular dynamics in studies of polymerase behavior is discussed.

Third Trimester Estrogens and Maternal Breast Cancer: Prospective Evidence.

Context: Full-term pregnancy is associated with a transient increase and life-time decrease in maternal breast cancer risk. Estrone (E1), estradiol (E2), and estriol (E3) are in high concentration during the third trimester. E1 and E2 metabolism produces carcinogenic intermediaries, and E3 metabolism does not. Objective: We tested the hypothesis that higher E3 in pregnancy is protective while higher E1 plus E2 increases risk. Design: Prospective case-cohort study (n = 620; 204 cases) nested in a 38-year follow-up of 15,528 pregnant women in the Child Health and Development Studies. We measured E1, E2, and E3 in archived third trimester serum and estimated associations with breast cancer. Setting: Northern California Kaiser members receiving obstetric care from 1959 to 1967. Main Outcome Measure: Breast cancer diagnosed through 1997. Results: Doubling of E1+E2 was associated with greater risk [hazard ratio (HR), 1.7; 95% confidence interval (CI), 1.2 to 2.4]. In contrast, doubling of E3 or the E3/E1+E2 ratio was associated with protection (HR, 0.7; 95% CI, 0.5 to 1.0; HR, 0.6; 95% CI, 0.4 to 0.8, respectively). Associations were stronger for diagnoses within 15 years after delivery compared with 16 to 38 years (Pinteraction = 0.0002) for gravidas >27 years at delivery vs ≤27 (Pinteraction = 0.01) and for primiparas vs multiparas (Pinteraction = 0.02). Conclusions: Relatively high third trimester E3 levels might protect parous women from breast cancer and E1 and E2 might enhance the risk. If findings are confirmed, third trimester pregnancy estrogens could help explain how parity affects breast cancer.

Improved Accuracy for Constant pH-REMD Simulations through Modification of Carboxylate Effective Radii.

The accuracy of computational models for simulating biomolecules under specific solution pH conditions is critical for properly representing the effect of pH in biological processes. Constant pH (CpH) simulations involving implicit solvent using the AMBER software often incorrectly estimate pKa values of aspartate and glutamate residues due to large effective radii stemming from the presence of dummy protons. These inaccuracies stem from problems in the sampled ensembles of titratable residues that can influence other observable pH-dependent behavior, such as conformational change. We investigate new radii assignments for atoms in titratable residues with carboxylate groups to mitigate the systematic overestimation in the current method. We find that decreased carboxylate radii correspond with increased agreement with experimentally derived pKa values for residues in hen egg-white lysozyme and Δ+PHS variants of staphylococcal nuclease (SNase) and improved conformation state sampling compared to experimentally described expectations of native-like structure. Our CpH simulations suggest that decreasing the effective radii of these carboxylate groups is essential for eliminating a significant source of systematic error that hurts the accuracy of both conformational and protonation state sampling with implicit solvent.

Design and computational support for the binding stability of a new CCR5/CXCR4 dual tropic inhibitor: Computational design of a CCR5/CXCR4 drug.

The human immunodeficiency virus (HIV) infects healthy human cells by binding to the glycoprotein cluster of differentiation 4 receptors on the surface of helper T-cells, along with either of two chemokine receptors, CC chemokine receptor type 5 (CCR5) or C-X-C chemokine receptor type 4 (CXCR4). Recently, a pyrazolo-piperdine ligand was synthesized and the corresponding biological data showed good binding to both chemokine receptors, effectively blocking HIV-1 entry. Here, we exhaustively assess the atomistic binding interactions of this compound with both CCR5 and CXCR4, and we find that binding is driven by π-stacking interactions between aromatic rings on the ligand and receptor residues, as well as electrostatic interactions involving the protonated piperidine nitrogen. However, these favorable binding interactions were partially offset by unfavorable desolvation of active site glutamates and aspartates, prompting our proposal of a new, synthetically-accessible derivative designed to increase the electrostatic interactions without compromising the π-stacking features.

Internal abstraction of dynemicin A: An MD approach.

Dynemicin A has the ability to undergo the Bergman cyclization, forming a para-benzyne moiety with the ability to induce DNA strand scission. This property of dynemicin A makes it a promising anti-tumor agent. Past research has shown conclusively that dynemicin A binds to and abstracts a hydrogen atom (H5') from the DNA backbone, but the molecular mechanism of the binding event is not fully understood. We have used AMBER Molecular Dynamics simulations to investigate the dynamics associated with the reaction mechanisms. Previously, two binding mechanisms have been proposed, of which the second is more supported: (1) dynemicin A intercalates between two base pairs and directly abstracts a hydrogen atom from DNA and (2) dynemicin A inserts into the minor groove and directly abstracts a hydrogen atom from DNA. We propose a third mechanism, where dynemicin A intercalates, then undergoes a proximate, intramolecular hydrogen atom abstraction (internal abstraction). While not studied here, the resulting radical would then subsequently abstract a hydrogen atom from DNA.

A molecular dynamics study of the binary complexes of APP, JIP1, and the cargo binding domain of KLC.

Mutations in the amyloid precursor protein (APP) are responsible for the formation of amyloid-ß peptides. These peptides play a role in Alzheimer's and other dementia-related diseases. The cargo binding domain of the kinesin-1 light chain motor protein (KLC1) may be responsible for transporting APP either directly or via interaction with C-jun N-terminal kinase-interacting protein 1 (JIP1). However, to date there has been no direct experimental or computational assessment of such binding at the atomistic level. We used molecular dynamics and free energy estimations to gauge the affinity for the binary complexes of KLC1, APP, and JIP1. We find that all binary complexes (KLC1:APP, KLC1:JIP1, and APP:JIP1) contain conformations with favorable binding free energies. For KLC1:APP the inclusion of approximate entropies reduces the favorability. This is likely due to the flexibility of the 42-residue APP protein. In all cases we analyze atomistic/residue driving forces for favorable interactions. Proteins 2017; 85:221-234. © 2016 Wiley Periodicals, Inc.